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Zhang A, Shang Q. Transcriptome Analysis of Early Lateral Root Formation in Tomato. PLANTS (BASEL, SWITZERLAND) 2024; 13:1620. [PMID: 38931052 PMCID: PMC11207605 DOI: 10.3390/plants13121620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/17/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Lateral roots (LRs) receive signals from the inter-root environment and absorb water and nutrients from the soil. Auxin regulates LR formation, but the mechanism in tomato remains largely unknown. In this study, 'Ailsa Craig' tomato LRs appeared on the third day and were unevenly distributed in primary roots. According to the location of LR occurrence, roots were divided into three equal parts: the shootward part of the root (RB), the middle part of the root (RM), and the tip part of the root (RT). Transverse sections of roots from days 1 to 6 revealed that the number of RB cells and the root diameter were significantly increased compared with RM and RT. Using roots from days 1 to 3, we carried out transcriptome sequencing analysis. Identified genes were classified into 16 co-expression clusters based on K-means, and genes in four associated clusters were highly expressed in RB. These four clusters (3, 5, 8, and 16) were enriched in cellulose metabolism, microtubule, and peptide metabolism pathways, all closely related to LR development. The four clusters contain numerous transcription factors linked to LR development including transcription factors of LATERAL ORGAN BOUNDRIES (LOB) and MADS-box families. Additionally, auxin-related genes GATA23, ARF7, LBD16, EXP, IAA4, IAA7, PIN1, PIN2, YUC3, and YUC4 were highly expressed in RB tissue. Free IAA content in 3 d RB was notably higher, reaching 3.3-5.5 ng/g, relative to RB in 1 d and 2 d. The LR number was promoted by 0.1 μM of exogenous IAA and inhibited by exogenous NPA. We analyzed the root cell state and auxin signaling module during LR formation. At a certain stage of pericycle cell development, LR initiation is regulated by auxin signaling modules IAA14-ARF7/ARF19-LBD16-CDKA1 and IAA14-ARF7/ARF19-MUS/MUL-XTR6/EXP. Furthermore, as a key regulatory factor, auxin regulates the process of LR initiation and LR primordia (LRP) through different auxin signaling pathway modules.
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Affiliation(s)
| | - Qingmao Shang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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Wang Z, Chen F, Li X, Cao H, Ding M, Zhang C, Zuo J, Xu C, Xu J, Deng X, Xiang Y, Soppe WJJ, Liu Y. Arabidopsis seed germination speed is controlled by SNL histone deacetylase-binding factor-mediated regulation of AUX1. Nat Commun 2016; 7:13412. [PMID: 27834370 PMCID: PMC5114640 DOI: 10.1038/ncomms13412] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 09/30/2016] [Indexed: 12/22/2022] Open
Abstract
Histone acetylation is known to affect the speed of seed germination, but the molecular regulatory basis of this remains ambiguous. Here we report that loss of function of two histone deacetylase-binding factors, SWI-INDEPENDENT3 (SIN3)-LIKE1 (SNL1) and SNL2, results in accelerated radicle protrusion and growth during seed germination. AUXIN RESISTANT 1 (AUX1) is identified as a key factor in this process, enhancing germination speed downstream of SNL1 and SNL2. AUX1 expression and histone H3 acetylation at lysines 9 and 18 is regulated by SNL1 and SNL2. The D-type cyclins encoding genes CYCD1;1 and CYCD4;1 display increased expression in AUX1 over-expression lines and the snl1snl2 double mutant. Accordingly, knockout of CYCD4;1 reduces seed germination speed of AUX1 over-expression lines and snl1snl2 suggesting the importance of cell cycling for radicle protrusion during seed germination. Together, our work identifies AUX1 as a link between histone acetylation mediated by SNL1 and SNL2, and radicle growth promoted by CYCD1;1 and CYCD4;1 during seed germination. Histone acetylation influences the speed of seed germination. Here, Wang et al. show that loss of the SNL1/SNL2 histone deacetylase binding factors accelerates seed germination and provide evidence that they act by regulating the expression of AUX1 which in turn influences cell division.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meng Ding
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaonan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jimei Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Xiang
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53115 Bonn, Germany
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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An early secretory pathway mediated by GNOM-LIKE 1 and GNOM is essential for basal polarity establishment in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2015; 112:E806-15. [PMID: 25646449 DOI: 10.1073/pnas.1424856112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF-defective mutants gnom-like 1 (gnl1-1) and gnom (van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER)-Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.
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Xu Y, Zhang S, Guo H, Wang S, Xu L, Li C, Qian Q, Chen F, Geisler M, Qi Y, Jiang DA. OsABCB14 functions in auxin transport and iron homeostasis in rice (Oryza sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:106-17. [PMID: 24798203 DOI: 10.1111/tpj.12544] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/15/2014] [Accepted: 04/24/2014] [Indexed: 05/04/2023]
Abstract
Members of the ATP Binding Cassette B/Multidrug-Resistance/P-glyco-protein (ABCB/MDR/PGP) subfamily were shown to function primarily in Oryza sativa (rice) auxin transport; however, none of the rice ABCB transporters have been functionally characterized. Here, we describe that a knock-down of OsABCB14 confers decreased auxin concentrations and polar auxin transport rates, conferring insensitivity to 2,4-dichlorophenoxyacetic acid (2,4-D) and indole-3-acetic acid (IAA). OsABCB14 displays enhanced specific auxin influx activity in yeast and protoplasts prepared from rice knock-down alleles. OsABCB14 is localized at the plasma membrane, pointing to an important directionality under physiological conditions. osabcb14 mutants were surprisingly found to be insensitive to iron deficiency treatment (-Fe). Their Fe concentration is higher and upregulation of Fe deficiency-responsive genes is lower in osabcb14 mutants than in wild-type rice (Nipponbare, NIP). Taken together, our results strongly support the role of OsABCB14 as an auxin influx transporter involved in Fe homeostasis. The functional characterization of OsABCB14 provides insights in monocot auxin transport and its relationship to Fe nutrition.
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Affiliation(s)
- Yanxia Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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Xu A, Zhang W, Wen CK. ENHANCING ctr1-10 ETHYLENE RESPONSE2 is a novel allele involved in CONSTITUTIVE TRIPLE-RESPONSE1-mediated ethylene receptor signaling in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:48. [PMID: 24529183 PMCID: PMC3933193 DOI: 10.1186/1471-2229-14-48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 02/12/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND The signal output of ethylene receptor family members is mediated by unknown mechanisms to activate the Raf-like protein CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) in negatively regulating ethylene signaling. The physical interaction between the ethylene receptor histidine kinase (HK) domain and CTR1 N terminus is essential to the CTR1-mediated receptor signal output. To advance our knowledge of the involvement of CTR1-mediated ethylene receptor signaling, we performed a genetic screen for mutations that enhanced the constitutive ethylene response in the weak ctr1-10 allele. RESULTS We isolated a loss-of-function allele of ENHANCING ctr1-10 ETHYLENE RESPONSE2 (ECR2) and found that ecr2-1 ctr1-10 and the strong allele ctr1-1 conferred a similar, typical constitutive ethylene response phenotype. Genetic analyses and transformation studies suggested that ECR2 acts downstream of the ethylene receptors and upstream of the transcription factors ETHYLENE INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1), which direct the expression of ethylene response genes. Signal output by the N terminus of the ethylene receptor ETHYLENE RESPONSE1 (ETR1) can be mediated by a pathway independent of CTR1. Expression of the N terminus of the ethylene-insensitive etr1-1 but not the full-length isoform rescued the ecr2-1 ctr1-10 phenotype, which indicates the involvement of ECR2 in CTR1-mediated but not -independent, ethylene receptor signaling. ECR2 was mapped to the centromere region on chromosome 2. With incomplete sequence and annotation information and rare chromosome recombination events in this region, the cloning of ECR2 is challenging and still in progress. CONCLUSIONS ECR2 is a novel allele involved in the ethylene receptor signaling that is mediated by CTR1. CTR1 activation by ethylene receptors may require ECR2 for suppressing the ethylene response.
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Affiliation(s)
- Aibei Xu
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Wei Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Chi-Kuang Wen
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
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Wang F, Cui X, Sun Y, Dong CH. Ethylene signaling and regulation in plant growth and stress responses. PLANT CELL REPORTS 2013; 32:1099-109. [PMID: 23525746 DOI: 10.1007/s00299-013-1421-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 02/28/2013] [Accepted: 03/09/2013] [Indexed: 05/19/2023]
Abstract
Gaseous phytohormone ethylene affects many aspects of plant growth and development. The ethylene signaling pathway starts when ethylene binds to its receptors. Since the cloning of the first ethylene receptor ETR1 from Arabidopsis, a large number of studies have steadily improved our understanding of the receptors and downstream components in ethylene signal transduction pathway. This article reviews the regulation of ethylene receptors, signal transduction, and the posttranscriptional modulation of downstream components. Functional roles and importance of the ethylene signaling components in plant growth and stress responses are also discussed. Cross-reactions of ethylene with auxin and other phytohormones in plant organ growth will be analyzed. The studies of ethylene signaling in plant growth, development, and stress responses in the past decade greatly advanced our knowledge of how plants respond to endogenous signals and environmental factors.
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Affiliation(s)
- Feifei Wang
- College of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, People's Republic of China
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