1
|
Li Q, Li F, Song X, Lu N, Jing X, Wen H, Ma P, Zhang H, Yao W, Wang X, Zhang M. Pan-cancer analysis of ARFs family and ARF5 promoted the progression of hepatocellular carcinoma. Heliyon 2024; 10:e29099. [PMID: 38617932 PMCID: PMC11015141 DOI: 10.1016/j.heliyon.2024.e29099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/16/2024] Open
Abstract
Background ARF family proteins are a kind of small GTPases, which are involved in regulating a variety of basic functions of cells. In recent years, the role and molecular regulatory mechanisms of ARFs in tumor progression have received increasing attention, and research reports on most of their family members are increasing. However, research on the clinical and pathological relevance of ARF5 in cancer, especially in hepatocellular carcinoma, still needs to be improved. Methods RNA-seq data in the Cancer Genome Atlas (TCGA) and genome tissue expression (GTEx) databases were used to analyze the expression and pathological data of ARFs family in Pan-cancer. Kaplan-Meier and Cox regression were used for prognostic analysis of ARF5 and Pan-cancer. Combined with ImmuCellAI database and TIMER2 database, the relationship between ARF5 expression and immune cell tumor infiltration in hepatocellular carcinoma (HCC) was analyzed. WGCNA is used to construct the co-expression gene network related to ARF5 expression in HCC and screen important modules and central genes. GO and KEGG path enrichment analysis were carried out for the genes in the modules with clinical significance. GSEA analysis was performed to take into account the role of genes with small differences. Finally, ceRNA network analysis was used to explore the molecular mechanism of miRNAs and lncRNAs regulating ARF5 expression. Results ARFs family (ARF1, ARF3, ARF4, ARF5, ARF6) are generally highly expressed in Pan-cancer. ARF5 is significantly highly expressed in 29 cancers, and the high expression of ARF5 in HCC patients is significantly negatively correlated with OS, DFI, PFI and DSS, which may lead to cancer deterioration by participating in tumor immune infiltration of HCC. Through WGCNA analysis, the expression of ARF5 in HCC may be involved in many cellular processes that consume a lot of energy, such as ribosome formation, RNA and protein synthesis and lipids, as well as COVID-19, nonalcoholic fatty liver, neurodegenerative diseases and other disease pathways. Conclusion ARFs, especially ARF5, are overexpressed in many human tumors. This study shows for the first time that ARF5 is significantly correlated with the poor prognosis of HCC patients, which may play a role as an oncogene, suggesting that ARF5 has the potential as a biomarker for the diagnosis and treatment of HCC.
Collapse
Affiliation(s)
- Qian Li
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Fang Li
- Institute of Genetics and Development Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Xinqiu Song
- Medical College of Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Ning Lu
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Xintao Jing
- Institute of Genetics and Development Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Hua Wen
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Peihan Ma
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Hua Zhang
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Wenzhu Yao
- Xi'an Medical University, Xi'an, 710021, Shaanxi, China
| | - Xiaofei Wang
- Biomedical Experimental Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Mingxin Zhang
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
- Shaanxi University of Traditional Chinese Medicine, Xianyang, 712046, Shaanxi, China
| |
Collapse
|
2
|
Yamamoto N, Chen Z, Guo Y, Tong W, Yu Z, Wu Y, Peng Z, Yang Z. Gene co-expression modules behind the three-pistil formation in wheat. Funct Integr Genomics 2023; 23:123. [PMID: 37055658 DOI: 10.1007/s10142-023-01052-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
Multi-pistil trait in wheat is of great potential value in plant development research and crop breeding. Our previous studies identified the Pis1 locus that causes three pistils in wheat by genetic mapping using multiple DNA marker systems. However, there are still 26 candidate genes on the locus, and the causal gene remains to be found. In this study, we aimed to approach the molecular mechanism of multi-pistil formation. Comparative RNA sequencing (RNA-Seq) during the pistil formation was undertaken in four wheat lines: a three-pistil mutant TP, a single-pistil TILLING mutant of TP (SP), a three-pistil near-isogenic line CM28TP with the background of cultivar Chunmai 28 (CM28), and CM28. Electron microscopic analysis specified probable developmental stages of young spikes for the three-pistil formation. mRNA sequencing in the young spikes of the four lines represented 253 down-regulated genes and 98 up-regulated genes in both three-pistil lines, which included six potential genes for ovary development. Weighted gene co-expression analysis represented three-pistil trait-associated transcription factor-like genes, among which one hub gene, ARF5, was the most highlighted. ARF5 is on the Pis1 locus and an orthologue of MONOPTEROS which mediates tissue development in Arabidopsis. qRT-PCR validation implies that the deficiency of ARF5 underlies the three-pistil formation in wheat.
Collapse
Affiliation(s)
- Naoki Yamamoto
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zhenyong Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Yuhuan Guo
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Wurina Tong
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zhouyuan Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Yichao Wu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang University, Xichang, 615000, China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China.
| |
Collapse
|
3
|
Galibina NA, Tarelkina TV, Chirva OV, Moshchenskaya YL, Nikerova KM, Ivanova DS, Semenova LI, Serkova AA, Novitskaya LL. Molecular Genetic Characteristics of Different Scenarios of Xylogenesis on the Example of Two Forms of Silver Birch Differing in the Ratio of Structural Elements in the Xylem. Plants (Basel) 2021; 10:1593. [PMID: 34451638 DOI: 10.3390/plants10081593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022]
Abstract
Silver birch (Betula pendula Roth) is an economically important species in Northern Europe. The current research focused on the molecular background of different xylogenesis scenarios in the birch trunks. The study objects were two forms of silver birch, silver birch trees, and Karelian birch trees; the latter form is characterized by the formation of two types of wood, non-figured (straight-grained) and figured, respectively, while it is currently not clear which factors cause this difference. We identified VND/NST/SND genes that regulate secondary cell wall biosynthesis in the birch genome and revealed differences in their expression in association with the formation of xylem with different ratios of structural elements. High expression levels of BpVND7 accompanied differentiation of the type of xylem which is characteristic of the species. At the same time, the appearance of figured wood was accompanied by the low expression levels of the VND genes and increased levels of expression of NST and SND genes. We identified BpARF5 as a crucial regulator of auxin-dependent vascular patterning and its direct target—BpHB8. A decrease in the BpARF5 level expression in differentiating xylem was a specific characteristic of both Karelian birch with figured and non-figured wood. Decreased BpARF5 level expression in non-figured trees accompanied by decreased BpHB8 and VND/NST/SND expression levels compared to figured Karelian birch trees. According to the results obtained, we suggested silver birch forms differing in wood anatomy as valuable objects in studying the regulation of xylogenesis.
Collapse
|
4
|
Zhang C, Fan L, Le BH, Ye P, Mo B, Chen X. Regulation of ARGONAUTE10 Expression Enables Temporal and Spatial Precision in Axillary Meristem Initiation in Arabidopsis. Dev Cell 2020; 55:603-616.e5. [PMID: 33232670 DOI: 10.1016/j.devcel.2020.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 06/16/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022]
Abstract
Axillary meristems (AMs) give rise to lateral shoots and are critical to plant architecture. Understanding how developmental cues and environmental signals impact AM development will enable the improvement of plant architecture in agriculture. Here, we show that ARGONAUTE10 (AGO10), which sequesters miR165/166, promotes AM development through the miR165/166 target gene REVOLUTA. We reveal that AGO10 expression is precisely controlled temporally and spatially by auxin, brassinosteroids, and light to result in AM initiation only in the axils of leaves at a certain age. AUXIN RESPONSE FACTOR 5 (ARF5) activates while BRASSINAZOLE-RESISTANT 1 (BZR1) and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) repress AGO10 transcription directly. In axils of young leaves, BZR1 and PIF4 repress AGO10 expression to prevent AM initiation. In axils of older leaves, ARF5 upregulates AGO10 expression to promote AM initiation. Our results uncover the spatiotemporal control of AM development through the cooperation of hormones and light converging on a regulator of microRNA.
Collapse
Affiliation(s)
- Cui Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lusheng Fan
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Brandon H Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Peiyi Ye
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
5
|
Yue P, Lu Q, Liu Z, Lv T, Li X, Bu H, Liu W, Xu Y, Yuan H, Wang A. Auxin-activated Md ARF5 induces the expression of ethylene biosynthetic genes to initiate apple fruit ripening. New Phytol 2020; 226:1781-1795. [PMID: 32083754 PMCID: PMC7317826 DOI: 10.1111/nph.16500] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 05/18/2023]
Abstract
The gaseous plant hormone ethylene induces the ripening of climacteric fruit, including apple (Malus domestica). Another phytohormone, auxin, is known to promote ethylene production in many horticultural crops, but the regulatory mechanism remains unclear. Here, we found that auxin application induces ethylene production in apple fruit before the stage of commercial harvest, when they are not otherwise capable of ripening naturally. The expression of MdARF5, a member of the auxin response factor transcription factor (TF) family involved in the auxin signaling pathway, was enhanced by treatment with the synthetic auxin naphthaleneacetic acid (NAA). Further studies revealed that MdARF5 binds to the promoter of MdERF2, encoding a TF in the ethylene signaling pathway, as well as the promoters of two 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes (MdACS3a and MdACS1) and an ACC oxidase (ACO) gene, MdACO1, all of which encode key steps in ethylene biosynthesis, thereby inducing their expression. We also observed that auxin-induced ethylene production was dependent on the methylation of the MdACS3a promoter. Our findings reveal that auxin induces ethylene biosynthesis in apple fruit through activation of MdARF5 expression.
Collapse
Affiliation(s)
- Pengtao Yue
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Qian Lu
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Zhi Liu
- Liaoning Institute of PomologyXiongyue115009China
| | - Tianxing Lv
- Liaoning Institute of PomologyXiongyue115009China
| | - Xinyue Li
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Haidong Bu
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Weiting Liu
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Yaxiu Xu
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Hui Yuan
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| | - Aide Wang
- College of HorticultureShenyang Agricultural UniversityShenyang110866China
| |
Collapse
|
6
|
Agarwal P, Singh PC, Chaudhry V, Shirke PA, Chakrabarty D, Farooqui A, Nautiyal CS, Sane AP, Sane VA. PGPR-induced OsASR6 improves plant growth and yield by altering root auxin sensitivity and the xylem structure in transgenic Arabidopsis thaliana. J Plant Physiol 2019; 240:153010. [PMID: 31352021 DOI: 10.1016/j.jplph.2019.153010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 05/02/2023]
Abstract
Plant-growth-promoting rhizobacteria (PGPR) improve plant growth by altering the root architecture, although the mechanisms underlying this alteration have yet to be unravelled. Through microarray analysis of PGPR-treated rice roots, a large number of differentially regulated genes were identified. Ectopic expression of one of these genes, OsASR6 (ABA STRESS RIPENING6), had a remarkable effect on plant growth in Arabidopsis. Transgenic lines over-expressing OsASR6 had larger leaves, taller inflorescence bolts and greater numbers of siliques and seeds. The most prominent effect was observed in root growth, with the root biomass increasing four-fold compared with the shoot biomass increase of 1.7-fold. Transgenic OsASR6 over-expressing plants showed higher conductance, transpiration and photosynthesis rates, leading to an ˜30% higher seed yield compared with the control. Interestingly, OsASR6 expression led to alterations in the xylem structure, an increase in the xylem vessel size and altered lignification, which correlated with higher conductance. OsASR6 is activated by auxin and, in turn, increases auxin responses and root auxin sensitivity, as observed by the increased expression of auxin-responsive genes, such as SAUR32 and PINOID, and the key auxin transcription factor, ARF5. Collectively, these phenomena led to an increased root density. The effects of OsASR6 expression largely mimic the beneficial effects of PGPRs in rice, indicating that OsASR6 activation may be a key factor governing PGPR-mediated changes in rice. OsASR6 is a potential candidate for the manipulation of rice for improved productivity.
Collapse
Affiliation(s)
- Pallavi Agarwal
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow, 226001, India; Integral University, Lucknow, India
| | - Poonam C Singh
- Microbiology Division, CSIR- National Botanical Research Institute, Lucknow, 226001, India
| | - Vasvi Chaudhry
- Microbiology Division, CSIR- National Botanical Research Institute, Lucknow, 226001, India
| | - Pramod A Shirke
- Plant Physiology, CSIR- National Botanical Research Institute, Lucknow, 226001, India
| | - Debasis Chakrabarty
- Genetics and Molecular Biology Division, CSIR- National Botanical Research Institute, Lucknow-226001, India
| | | | | | - Aniruddha P Sane
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow, 226001, India
| | - Vidhu A Sane
- Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow, 226001, India.
| |
Collapse
|
7
|
Xu C, Shen Y, He F, Fu X, Yu H, Lu W, Li Y, Li C, Fan D, Wang HC, Luo K. Auxin-mediated Aux/IAA-ARF-HB signaling cascade regulates secondary xylem development in Populus. New Phytol 2019; 222:752-767. [PMID: 30582614 DOI: 10.1111/nph.15658] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/14/2018] [Indexed: 05/21/2023]
Abstract
Wood development is strictly regulated by various phytohormones and auxin plays a central regulatory role in this process. However, how the auxin signaling is transducted in developing secondary xylem during wood formation in tree species remains unclear. Here, we identified an Aux/INDOLE-3-ACETIC ACID 9 (IAA9)-AUXIN RESPONSE FACTOR 5 (ARF5) module in Populus tomentosa as a key mediator of auxin signaling to control early developing xylem development. PtoIAA9, a canonical Aux/IAA gene, is predominantly expressed in vascular cambium and developing secondary xylem and induced by exogenous auxin. Overexpression of PtoIAA9m encoding a stabilized IAA9 protein significantly represses secondary xylem development in transgenic poplar. We further showed that PtoIAA9 interacts with PtoARF5 homologs via the C-terminal III/IV domains. The truncated PtoARF5.1 protein without the III/IV domains rescued defective phenotypes caused by PtoIAA9m. Expression analysis showed that the PtoIAA9-PtoARF5 module regulated the expression of genes associated with secondary vascular development in PtoIAA9m- and PtoARF5.1-overexpressing plants. Furthermore, PtoARF5.1 could bind to the promoters of two Class III homeodomain-leucine zipper (HD-ZIP III) genes, PtoHB7 and PtoHB8, to modulate secondary xylem formation. Taken together, our results suggest that the Aux/IAA9-ARF5 module is required for auxin signaling to regulate wood formation via orchestrating the expression of HD-ZIP III transcription factors in poplar.
Collapse
Affiliation(s)
- Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yun Shen
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Fu He
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Hong Yu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Wanxiang Lu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yongli Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chaofeng Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Hua Cassan Wang
- UMR5546, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III Paul Sabatier, CNRS, UPS, 31326, Castanet-Tolosan, France
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| |
Collapse
|
8
|
Wójcikowska B, Gaj MD. Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. Plant Cell Rep 2017; 36:843-858. [PMID: 28255787 PMCID: PMC5486788 DOI: 10.1007/s00299-017-2114-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/01/2017] [Indexed: 05/18/2023]
Abstract
Extensive modulation of numerous ARF transcripts in the embryogenic culture of Arabidopsis indicates a substantial role of auxin signaling in the mechanism of somatic embryogenesis induction. Somatic embryogenesis (SE) is induced by auxin in plants and auxin signaling is considered to play a key role in the molecular mechanism that controls the embryogenic transition of plant somatic cells. Accordingly, the expression of AUXIN RESPONSE FACTOR (ARF) genes in embryogenic culture of Arabidopsis was analyzed. The study revealed that 14 of the 22 ARFs were transcribed during SE in Arabidopsis. RT-qPCR analysis indicated that the expression of six ARFs (ARF5, ARF6, ARF8, ARF10, ARF16, and ARF17) was significantly up-regulated, whereas five other genes (ARF1, ARF2, ARF3, ARF11, and ARF18) were substantially down-regulated in the SE-induced explants. The activity of ARFs during SE was also monitored with GFP reporter lines and the ARFs that were expressed in areas of the explants engaged in SE induction were detected. A functional test of ARFs transcribed during SE was performed and the embryogenic potential of the arf mutants and overexpressor lines was evaluated. ARFs with a significantly modulated expression during SE coupled with an impaired embryogenic response of the relevant mutant and/or overexpressor line, including ARF1, ARF2, ARF3, ARF5, ARF6, ARF8, and ARF11 were indicated as possibly being involved in SE induction. The study provides evidence that embryogenic induction strongly depends on ARFs, which are key regulators of the auxin signaling. Some clues on the possible functions of the candidate ARFs, especially ARF5, in the mechanism of embryogenic transition are discussed. The results provide guidelines for further research on the auxin-related functional genomics of SE and the developmental plasticity of somatic cells.
Collapse
Affiliation(s)
- Barbara Wójcikowska
- Department of Genetics, University of Silesia, ul. Jagiellońska 28, 40-032, Katowice, Poland
| | - Małgorzata D Gaj
- Department of Genetics, University of Silesia, ul. Jagiellońska 28, 40-032, Katowice, Poland.
| |
Collapse
|
9
|
Zheng K, Wang Y, Zhang N, Jia Q, Wang X, Hou C, Chen JG, Wang S. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci 2017; 8:1813. [PMID: 29114256 PMCID: PMC5660721 DOI: 10.3389/fpls.2017.01813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/05/2017] [Indexed: 05/05/2023]
Abstract
Auxin regulates nearly all aspects of plant growth and development including cell division, cell elongation and cell differentiation, which are achieved largely by rapid regulation of auxin response genes. However, the functions of a large number of auxin response genes remain uncharacterized. Paclobutrazol Resistance (PRE) proteins are non-DNA binding basic helix-loop-helix transcription factors that have been shown to be involved in gibberellin and brassinosteroid signaling, and light responses in Arabidopsis. Here, we provide molecular and genetic evidence that PRE6, one of the six PRE genes in Arabidopsis, is an auxin response gene, and that PRE6 is involved in the regulation of auxin signaling. By using quantitative RT-PCR, we showed that the expression level of PRE6 was increased in response to exogenously applied IAA. GUS staining results also showed that the expression of GUS reporter gene in the PRE6p:GUS transgenic seedlings was elevated in response to auxin. Phenotypic analysis showed that overexpression of PRE6 in Arabidopsis resulted in auxin-related phenotypes including elongated hypocotyl and primary roots, and reduced number of lateral roots when compared with the Col wild type seedlings, whereas opposite phenotypes were observed in the pre6 mutants. Further analysis showed that PRE6 overexpression plants were hyposensitive, whereas pre6 mutants were hypersensitive to auxin in root and hypocotyl elongation and lateral root formation assays. By using protoplasts transfection, we showed that PRE6 functions as a transcriptional repressor. Consistent with this, the expression of the auxin response reporter DR5:GUS was decreased in PRE6 overexpression lines, but increased in pre6 mutants. When co-transfected into protoplasts, ARF5 and ARF8 activated the expression of the PRE6p:GUS reporter. Chromatin immunoprecipitation assays showed that ARF5 and ARF8 can be recruited to the promoter regions of PRE6. Taken together, these results suggest that PRE6 is an auxin response gene whose expression is directly regulated by ARF5 and ARF8, and that PRE6 is a transcriptional repressor that negatively regulates auxin responses in Arabidopsis.
Collapse
Affiliation(s)
- Kaijie Zheng
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Na Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Qiming Jia
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Chunjiang Hou
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- *Correspondence: Shucai Wang,
| |
Collapse
|
10
|
Bhatia N, Bozorg B, Larsson A, Ohno C, Jönsson H, Heisler MG. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr Biol 2016; 26:3202-3208. [PMID: 27818174 PMCID: PMC5154752 DOI: 10.1016/j.cub.2016.09.044] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/29/2016] [Accepted: 09/22/2016] [Indexed: 12/13/2022]
Abstract
The periodic formation of plant organs such as leaves and flowers gives rise to intricate patterns that have fascinated biologists and mathematicians alike for hundreds of years [1]. The plant hormone auxin plays a central role in establishing these patterns by promoting organ formation at sites where it accumulates due to its polar, cell-to-cell transport [2, 3, 4, 5, 6]. Although experimental evidence as well as modeling suggest that feedback from auxin to its transport direction may help specify phyllotactic patterns [7, 8, 9, 10, 11, 12], the nature of this feedback remains unclear [13]. Here we reveal that polarization of the auxin efflux carrier PIN-FORMED 1 (PIN1) is regulated by the auxin response transcription factor MONOPTEROS (MP) [14]. We find that in the shoot, cell polarity patterns follow MP expression, which in turn follows auxin distribution patterns. By perturbing MP activity both globally and locally, we show that localized MP activity is necessary for the generation of polarity convergence patterns and that localized MP expression is sufficient to instruct PIN1 polarity directions non-cell autonomously, toward MP-expressing cells. By expressing MP in the epidermis of mp mutants, we further show that although MP activity in a single-cell layer is sufficient to promote polarity convergence patterns, MP in sub-epidermal tissues helps anchor these polarity patterns to the underlying cells. Overall, our findings reveal a patterning module in plants that determines organ position by orienting transport of the hormone auxin toward cells with high levels of MP-mediated auxin signaling. We propose that this feedback process acts broadly to generate periodic plant architectures. Auxin-regulated MP expression and activity predict PIN1 polarity changes at the SAM Localized MP activity is necessary to mediate periodic organ formation MP orients PIN1 polarity non-cell autonomously to promote local auxin accumulation Sub-epidermal MP activity is required to stabilize auxin distribution patterns
Collapse
Affiliation(s)
- Neha Bhatia
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Behruz Bozorg
- Computational Biology and Biological Physics Group, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - André Larsson
- Computational Biology and Biological Physics Group, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Carolyn Ohno
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Henrik Jönsson
- Computational Biology and Biological Physics Group, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden; Sainsbury Laboratory and Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Marcus G Heisler
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Biological Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| |
Collapse
|
11
|
Odat O, Gardiner J, Sawchuk MG, Verna C, Donner TJ, Scarpella E. Characterization of an allelic series in the MONOPTEROS gene of Arabidopsis. Genesis 2013; 52:127-33. [PMID: 24281793 DOI: 10.1002/dvg.22729] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 11/09/2022]
Abstract
Patterning of numerous features of plants depends on transduction of the auxin signal. Auxin signaling is mediated by several pathways, the best understood of which relies on the function of the MONOPTEROS (MP) gene. Seven mp mutant alleles have been described in the widely used Columbia background of Arabidopsis: two extensively characterized and five only partially characterized. One of these five mp alleles appears to be extinct and thus unavailable for analysis. We show that two of the four remaining, partially characterized mp alleles reported to be in the Columbia background are in fact not in this background. We extend characterization of the remaining two Columbia alleles of mp, and we identify and characterize four new alleles of mp in the Columbia background, among which the first low-expression allele of mp and the strongest Columbia allele of mp. These genetic resources provide the research community with new experimental opportunities for insight into the function of MP-dependent auxin signaling in plant development.
Collapse
Affiliation(s)
- Osama Odat
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | | | | | | | | |
Collapse
|