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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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Kuznetsova X, Dodueva I, Afonin A, Gribchenko E, Danilov L, Gancheva M, Tvorogova V, Galynin N, Lutova L. Whole-Genome Sequencing and Analysis of Tumour-Forming Radish ( Raphanus sativus L.) Line. Int J Mol Sci 2024; 25:6236. [PMID: 38892425 PMCID: PMC11172632 DOI: 10.3390/ijms25116236] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.
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Affiliation(s)
- Xenia Kuznetsova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Irina Dodueva
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Alexey Afonin
- All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia (E.G.)
| | - Emma Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia (E.G.)
| | - Lavrentii Danilov
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Maria Gancheva
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Varvara Tvorogova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
| | - Nikita Galynin
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
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Łabuz J, Banaś AK, Zgłobicki P, Bażant A, Sztatelman O, Giza A, Lasok H, Prochwicz A, Kozłowska-Mroczek A, Jankowska U, Hermanowicz P. Phototropin2 3'UTR overlaps with the AT5G58150 gene encoding an inactive RLK kinase. BMC PLANT BIOLOGY 2024; 24:55. [PMID: 38238701 PMCID: PMC10795372 DOI: 10.1186/s12870-024-04732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND This study examines the biological implications of an overlap between two sequences in the Arabidopsis genome, the 3'UTR of the PHOT2 gene and a putative AT5G58150 gene, encoded on the complementary strand. AT5G58150 is a probably inactive protein kinase that belongs to the transmembrane, leucine-rich repeat receptor-like kinase family. Phot2 is a membrane-bound UV/blue light photoreceptor kinase. Thus, both proteins share their cellular localization, on top of the proximity of their loci. RESULTS The extent of the overlap between 3'UTR regions of AT5G58150 and PHOT2 was found to be 66 bp, using RACE PCR. Both the at5g58150 T-DNA SALK_093781C (with insertion in the promoter region) and 35S::AT5G58150-GFP lines overexpress the AT5G58150 gene. A detailed analysis did not reveal any substantial impact of PHOT2 or AT5G58150 on their mutual expression levels in different light and osmotic stress conditions. AT5G58150 is a plasma membrane protein, with no apparent kinase activity, as tested on several potential substrates. It appears not to form homodimers and it does not interact with PHOT2. Lines that overexpress AT5G58150 exhibit a greater reduction in lateral root density due to salt and osmotic stress than wild-type plants, which suggests that AT5G58150 may participate in root elongation and formation of lateral roots. In line with this, mass spectrometry analysis identified proteins with ATPase activity, which are involved in proton transport and cell elongation, as putative interactors of AT5G58150. Membrane kinases, including other members of the LRR RLK family and BSK kinases (positive regulators of brassinosteroid signalling), can also act as partners for AT5G58150. CONCLUSIONS AT5G58150 is a membrane protein that does not exhibit measurable kinase activity, but is involved in signalling through interactions with other proteins. Based on the interactome and root architecture analysis, AT5G58150 may be involved in plant response to salt and osmotic stress and the formation of roots in Arabidopsis.
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Affiliation(s)
- Justyna Łabuz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland.
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Giza
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Hanna Lasok
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Aneta Prochwicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Anna Kozłowska-Mroczek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Paweł Hermanowicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
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Zhao P, Zhang J, Chen S, Zhang Z, Wan G, Mao J, Wang Z, Tan S, Xiang C. ERF1 inhibits lateral root emergence by promoting local auxin accumulation and repressing ARF7 expression. Cell Rep 2023; 42:112565. [PMID: 37224012 DOI: 10.1016/j.celrep.2023.112565] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/28/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Lateral roots (LRs) are crucial for plants to sense environmental signals in addition to water and nutrient absorption. Auxin is key for LR formation, but the underlying mechanisms are not fully understood. Here, we report that Arabidopsis ERF1 inhibits LR emergence by promoting local auxin accumulation with altered distribution and regulating auxin signaling. Loss of ERF1 increases LR density compared with the wild type, whereas ERF1 overexpression causes the opposite phenotype. ERF1 enhances auxin transport by upregulating PIN1 and AUX1, resulting in excessive auxin accumulation in the endodermal, cortical, and epidermal cells surrounding LR primordia. Furthermore, ERF1 represses ARF7 transcription, thereby downregulating the expression of cell-wall remodeling genes that facilitate LR emergence. Together, our study reveals that ERF1 integrates environmental signals to promote local auxin accumulation with altered distribution and repress ARF7, consequently inhibiting LR emergence in adaptation to fluctuating environments.
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Affiliation(s)
- Pingxia Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
| | - Jing Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Siyan Chen
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zisheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Guangyu Wan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Jieli Mao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zhen Wang
- College of Life Sciences, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Shutang Tan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Chengbin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
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5
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Liu M, Zhang Q, Jin R, Zhao P, Zhu X, Wang J, Yu Y, Tang Z. The Role of IAA in Regulating Root Architecture of Sweetpotato ( Ipomoea batatas [L.] Lam) in Response to Potassium Deficiency Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091779. [PMID: 37176837 PMCID: PMC10181447 DOI: 10.3390/plants12091779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Plants can adapt to the spatial heterogeneity of soil nutrients by changing the morphology and architecture of the root system. Here, we explored the role of auxin in the response of sweetpotato roots to potassium (K+) deficiency stress. Two sweetpotato cultivars, Xushu 32 (low-K-tolerant) and Ningzishu 1 (low-K-sensitive), were cultured in low K+ (0.1 mmol L-1, LK) and normal K+ (10 mmol L-1, CK) nutrient solutions. Compared with CK, LK reduced the dry mass, K+ content, and K+ accumulation in the two cultivars, but the losses of Xushu 32 were smaller than those of Ningzishu 1. LK also affected root growth, mainly impairing the length, surface area, forks number, and crossings number. However, Xushu 32 had significantly higher lateral root length, density, and surface area than Ningzishu 1, closely related to the roots' higher indole-3-acetic acid (IAA) content. According to the qPCR results, Xushu 32 synthesized more IAA (via IbYUC8 and IbTAR2) in leaves but transported and accumulated in roots through polar transport (via IbPIN1, IbPIN3, and IbAUX1). It was also associated with the upregulation of auxin signaling pathway genes (IbIAA4 and IbIAA8) in roots. These results imply that IAA participates in the formation of lateral roots and the change in root architecture during the tolerance to low K+ stress of sweetpotato, thus improving the absorption of K+ and the formation of biomass.
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Affiliation(s)
- Ming Liu
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Qiangqiang Zhang
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
| | - Rong Jin
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
| | - Peng Zhao
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
| | - Xiaoya Zhu
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
| | - Jing Wang
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
| | - Yongchao Yu
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
| | - Zhonghou Tang
- Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China
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Qian Y, Wang X, Liu Y, Wang X, Mao T. HY5 inhibits lateral root initiation in Arabidopsis through negative regulation of the microtubule-stabilizing protein TPXL5. THE PLANT CELL 2023; 35:1092-1109. [PMID: 36512471 PMCID: PMC10015163 DOI: 10.1093/plcell/koac358] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Tight control of lateral root (LR) initiation is vital for root system architecture and function. Regulation of cortical microtubule reorganization is involved in the asymmetric radial expansion of founder cells during LR initiation in Arabidopsis (Arabidopsis thaliana). However, critical genetic evidence on the role of microtubules in LR initiation is lacking and the mechanisms underlying this regulation are poorly understood. Here, we found that the previously uncharacterized microtubule-stabilizing protein TPX2-LIKE5 (TPXL5) participates in LR initiation, which is finely regulated by the transcription factor ELONGATED HYPOCOTYL5 (HY5). In tpxl5 mutants, LR density was decreased and more LR primordia (LRPs) remained in stage I, indicating delayed LR initiation. In particular, the cell width in the peripheral domain of LR founder cells after the first asymmetric cell division was larger in tpxl5 mutants than in the wild-type. Consistently, ordered transverse cortical microtubule arrays were not well generated in tpxl5 mutants. In addition, HY5 directly targeted the promoter of TPXL5 and downregulated TPXL5 expression. The hy5 mutant exhibited higher LR density and fewer stage I LRPs, indicating accelerated LR initiation. Such phenotypes were partially suppressed by TPXL5 knockout. Taken together, our data provide genetic evidence supporting the notion that cortical microtubules are essential for LR initiation and unravel a molecular mechanism underlying HY5 regulation of TPXL5-mediated microtubule reorganization and cell remodeling during LR initiation.
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Affiliation(s)
- Yanmin Qian
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohong Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yimin Liu
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangfeng Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Control of lateral root initiation by DA3 in Arabidopsis. Cell Rep 2023; 42:111913. [PMID: 36640335 DOI: 10.1016/j.celrep.2022.111913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/02/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
Lateral root (LR) initiation is controlled by the pericycle and the neighboring endodermis in Arabidopsis. Here, we demonstrate that UBIQUITIN-SPECIFIC PROTEASE14/DA3 regulates LR initiation by modulating auxin signaling in the pericycle and endodermis. DA3 negatively affects the mRNA and protein levels of AUXIN RESPONSE FACTOR7 (ARF7) and ARF19 in the pericycle and endodermis but positively regulates the protein stability of SHORT HYPOCOTYL 2 (SHY2/IAA3), an auxin signaling repressor, in the endodermis. We show that DA3 interacts with ARF7 and ARF19, inhibiting their binding to the locus of LATERAL ORGAN BOUNDARY DOMAIN16 (LBD16) to repress its expression in the pericycle. SHY2 also interacts with ARF7 and ARF19 in the endodermis and enhances the DA3 repressive effect on ARF7 and ARF19, thus modulating LBD16 expression in the pericycle. Overall, our findings show that DA3 acts with SHY2, ARF7, and ARF19 to coordinate auxin signaling in the pericycle and endodermis to control LR initiation in Arabidopsis.
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Zhao D, Jiao J, Du B, Liu K, Wang C, Ding Y. Volatile organic compounds from Lysinibacillus macroides regulating the seedling growth of Arabidopsis thaliana. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1997-2009. [PMID: 36573143 PMCID: PMC9789275 DOI: 10.1007/s12298-022-01268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Volatile organic compounds (VOCs) have the characteristics of long distance propagation, low concentration, perception, and indirect contact between organisms. In this experiment, Lysinibacillus macroides Xi9 was isolated from cassava residue, and the VOCs produced by this strain were analyzed by the SPME-GC-MS method, mainly including alcohols, esters, and alkanes. By inoculation of L. macroides Xi9, VOCs can promote the growth and change the root-system architecture of Arabidopsis seedlings. The results showed that the number of lateral roots, root density, and fresh weight of Arabidopsis seedlings were significantly higher (p ≤ 0.01), and the number of roots hair was also increased after exposure to strain Xi9. Compared with the control group, the transcriptome analysis of Arabidopsis seedlings treated with strain Xi9 for 5 days revealed a total of 508 genes differentially expressed (p < 0.05). After Gene Ontology enrichment analysis, it was found that genes encoding nitrate transport and assimilation, and the lateral root-related gene ANR1 were up-regulated. The content of NO3 - and amino acid in Arabidopsis seedlings were significantly higher from control group (p ≤ 0.01). Plant cell wall-related EXPA family genes and pectin lyase gene were up-regulated, resulting cell elongation of leaf. SAUR41 and up-regulation of its subfamily members, as well as the down-regulation of auxin efflux carrier protein PILS5 and auxin response factor 20 (ARF20) led to the accumulation of auxin. These results indicated that VOCs of strain Xi9 promote Arabidopsis seedlings growth and development by promoting nitrogen uptake, regulating auxin synthesis, and improving cell wall modification. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01268-3.
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Affiliation(s)
- Dongying Zhao
- College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Junhui Jiao
- College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Binghai Du
- College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
- Shandong Key Laboratory of Agricultural Microbiology, Tai’an, 271018 China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Tai’an, 271018 China
| | - Kai Liu
- College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
- Shandong Key Laboratory of Agricultural Microbiology, Tai’an, 271018 China
| | - Chengqiang Wang
- College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
- Shandong Key Laboratory of Agricultural Microbiology, Tai’an, 271018 China
| | - Yanqin Ding
- College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
- Shandong Key Laboratory of Agricultural Microbiology, Tai’an, 271018 China
- Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Tai’an, 271018 China
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Ahmad N, Ibrahim S, Tian Z, Kuang L, Wang X, Wang H, Dun X. Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:994666. [PMID: 36172562 PMCID: PMC9511887 DOI: 10.3389/fpls.2022.994666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Plants rely on root systems for nutrient uptake from soils. Marker-assisted selection helps breeders to select desirable root traits for effective nutrient uptake. Here, 12 root and biomass traits were investigated at the seedling stage under low nitrogen (LN), low phosphorus (LP), and low potassium (LK) conditions, respectively, in a recombinant inbred line (RIL) population, which was generated from Brassica napus L. Zhongshuang11 and 4D122 with significant differences in root traits and nutrient efficiency. Significant differences for all the investigated traits were observed among RILs, with high heritabilities (0.43-0.74) and high correlations between the different treatments. Quantitative trait loci (QTL) mapping identified 57, 27, and 36 loci, explaining 4.1-10.9, 4.6-10.8, and 4.9-17.4% phenotypic variances under LN, LP, and LK, respectively. Through QTL-meta analysis, these loci were integrated into 18 significant QTL clusters. Four major QTL clusters involved 25 QTLs that could be repeatedly detected and explained more than 10% phenotypic variances, including two NPK-common and two specific QTL clusters (K and NK-specific), indicating their critical role in cooperative nutrients uptake of N, P, and K. Moreover, 264 genes within the four major QTL clusters having high expressions in roots and SNP/InDel variations between two parents were identified as potential candidate genes. Thirty-eight of them have been reported to be associated with root growth and development and/or nutrient stress tolerance. These key loci and candidate genes lay the foundation for deeper dissection of the NPK starvation response mechanisms in B. napus.
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Affiliation(s)
- Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
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10
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Wang Y, Chen W, Ou Y, Zhu Y, Li J. Arabidopsis ROOT ELONGATION RECEPTOR KINASES negatively regulate root growth putatively via altering cell wall remodeling gene expression. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1502-1513. [PMID: 35587568 DOI: 10.1111/jipb.13282] [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: 01/15/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Receptor-like kinases (RLKs) play key roles in regulating various physiological aspects in plant growth and development. In Arabidopsis thaliana, there are at least 223 leucine-rich repeat (LRR) RLKs. The functions of the majority of RLKs in the LRR XI subfamily were previously revealed. Only three RLKs were not characterized. Here we report that two independent triple mutants of these RLKs, named ROOT ELONGATION RECEPTOR KINASES (REKs), exhibit increased cell numbers in the root apical meristem and enhanced cell size in the elongation and maturation zones. The promoter activities of a number of Quiescent Center marker genes are significantly up-regulated in the triple mutant. However, the promoter activities of several marker genes known to control root stem cell niche activities are not altered. RNA-seq analysis revealed that a number of cell wall remodeling genes are significantly up-regulated in the triple mutant. Our results suggest that these REKs play key roles in regulating root development likely via negatively regulating the expression of a number of key cell wall remodeling genes.
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Affiliation(s)
- Yanze Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Weiyue Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yang Ou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yingying Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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11
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Peng Y, Zuo W, Zhou H, Miao F, Zhang Y, Qin Y, Liu Y, Long Y, Ma S. EXPLICIT-Kinase: A gene expression predictor for dissecting the functions of the Arabidopsis kinome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1374-1393. [PMID: 35446465 DOI: 10.1111/jipb.13267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Protein kinases regulate virtually all cellular processes, but it remains challenging to determine the functions of all protein kinases, collectively called the "kinome", in any species. We developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome. Because the activities of many kinases can be regulated transcriptionally, their gene expression patterns provide clues to their functions. A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 non-kinase genes based on the expression of 994 kinases. The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples. It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways. Strikingly, these predictor kinases were often regulators of related pathways, as exemplified by those involved in cytokinesis, tissue development, and stress responses. Comparative analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and maize. As an example, we identified a conserved predictor kinase, RAF6, from a stomatal movement module. We verified that RAF6 regulates stomatal closure. It can directly interact with SLAC1, a key anion channel for stomatal closure, and modulate its channel activity. Our approach enables a systematic dissection of the functions of the Arabidopsis kinome.
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Affiliation(s)
- Yuming Peng
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Wanzhu Zuo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Hui Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Fenfen Miao
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yue Qin
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yi Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yu Long
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Shisong Ma
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
- School of Data Science, University of Science and Technology of China, Hefei, 230027, China
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12
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Yang G, Chen BX, Chen T, Chen JH, Lin XY, Yue XL, An LZ, Zhang H. BYPASS1-LIKE regulates lateral root initiation via exocytic vesicular trafficking-mediated PIN recycling in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:965-978. [PMID: 35249253 DOI: 10.1111/jipb.13243] [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: 11/26/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Auxin and auxin-mediated signaling pathways are known to regulate lateral root development. Although exocytic vesicle trafficking plays an important role in recycling the PIN-FORMED (PIN) auxin efflux carriers and in polar auxin transport during lateral root formation, the mechanistic details of these processes are not well understood. Here, we demonstrate that BYPASS1-LIKE (B1L) regulates lateral root initiation via exocytic vesicular trafficking-mediated PIN recycling in Arabidopsis thaliana. b1l mutants contained significantly more lateral roots than the wild type, primarily due to increased lateral root primordium initiation. Furthermore, the auxin signal was stronger in stage I lateral root primordia of b1l than in those of the wild type. Treatment with exogenous auxin and an auxin transport inhibitor indicated that the lateral root phenotype of b1l could be attributed to higher auxin levels and that B1L regulates auxin efflux. Indeed, compared to the wild type, C-terminally green fluorescent protein-tagged PIN1 and PIN3 accumulated at higher levels in b1l lateral root primordia. B1L interacted with the exocyst, and b1l showed defective PIN exocytosis. These observations indicate that B1L interacts with the exocyst to regulate PIN-mediated polar auxin transport and lateral root initiation in Arabidopsis.
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Affiliation(s)
- Gang Yang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Bi-Xia Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Chen
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jia-Hui Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiang-Yu Lin
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiu-Le Yue
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Li-Zhe An
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- School of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Hua Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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13
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Song M, Linghu B, Huang S, Li F, An R, Xie C, Zhu Y, Hu S, Mu J, Zhang Y. Genome-Wide Survey of Leucine-Rich Repeat Receptor-Like Protein Kinase Genes and CRISPR/Cas9-Targeted Mutagenesis BnBRI1 in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:865132. [PMID: 35498707 PMCID: PMC9039726 DOI: 10.3389/fpls.2022.865132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 05/19/2023]
Abstract
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) family represents the largest group of RLKs in plants and plays vital roles in plant growth, development and the responses to environmental stress. Although LRR-RLK families have been identified in many species, they have not yet been reported in B. napus. In this study, a total of 444 BnLRR-RLK genes were identified in the genome of Brassica napus cultivar "Zhongshuang 11" (ZS11), and classified into 22 subfamilies based on phylogenetic relationships and genome-wide analyses. Conserved motifs and gene structures were shared within but not between subfamilies. The 444 BnLRR-RLK genes were asymmetrically distributed on 19 chromosomes and exhibited specific expression profiles in different tissues and in response to stress. We identified six BnBRI1 homologs and obtained partial knockouts via CRISPR/Cas9 technology, generating semi-dwarf lines without decreased yield compared with controls. This study provides comprehensive insight of the LRR-RLK family in B. napus. Additionally, the semi-dwarf lines expand the "ideotype" germplasm resources and accelerate the breeding process for B. napus.
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Affiliation(s)
- Min Song
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Bin Linghu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Fang Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Changgen Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Yantao Zhu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- *Correspondence: Jianxin Mu,
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- Yanfeng Zhang,
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14
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Identification and Characterization of Short Crown Root 8, a Temperature-Sensitive Mutant Associated with Crown Root Development in Rice. Int J Mol Sci 2021; 22:ijms22189868. [PMID: 34576034 PMCID: PMC8465104 DOI: 10.3390/ijms22189868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Crown roots are essential for plants to obtain water and nutrients, perceive environmental changes, and synthesize plant hormones. In this study, we identified and characterized short crown root 8 (scr8), which exhibited a defective phenotype of crown root and vegetative development. Temperature treatment showed that scr8 was sensitive to temperature and that the mutant phenotypes were rescued when grown under low temperature condition (20 °C). Histological and EdU staining analysis showed that the crown root formation was hampered and that the root meristem activity was decreased in scr8. With map-based cloning strategy, the SCR8 gene was fine-mapped to an interval of 126.4 kb on chromosome 8. Sequencing analysis revealed that the sequence variations were only found in LOC_Os08g14850, which encodes a CC-NBS-LRR protein. Expression and inoculation test analysis showed that the expression level of LOC_Os08g14850 was significantly decreased under low temperature (20 °C) and that the resistance to Xanthomonas oryzae pv. Oryzae (Xoo) was enhanced in scr8. These results indicated that LOC_Os08g14850 may be the candidate of SCR8 and that its mutation activated the plant defense response, resulting in a crown root growth defect.
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15
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Gala HP, Lanctot A, Jean-Baptiste K, Guiziou S, Chu JC, Zemke JE, George W, Queitsch C, Cuperus JT, Nemhauser JL. A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana. THE PLANT CELL 2021; 33:2197-2220. [PMID: 33822225 PMCID: PMC8364244 DOI: 10.1093/plcell/koab101] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/31/2021] [Indexed: 05/20/2023]
Abstract
Root architecture is a major determinant of plant fitness and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied examples of plant organogenesis, yet there are still many unanswered questions about its earliest steps. Among the challenges faced in capturing these first molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. Single-cell sequencing methods afford the opportunity to isolate the specific transcriptional changes occurring in cells undergoing this fate transition. Using this approach, we successfully captured the transcriptomes of initiating lateral root primordia in Arabidopsis thaliana and discovered many upregulated genes associated with this process. We developed a method to selectively repress target gene transcription in the xylem pole pericycle cells where lateral roots originate and demonstrated that the expression of several of these targets is required for normal root development. We also discovered subpopulations of cells in the pericycle and endodermal cell files that respond to lateral root initiation, highlighting the coordination across cell files required for this fate transition.
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Affiliation(s)
- Hardik P. Gala
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Amy Lanctot
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Jonah C. Chu
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Joseph E. Zemke
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Wesley George
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Josh T. Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Author for correspondence: (J.T.C.); (J.L.N.)
| | - Jennifer L. Nemhauser
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Author for correspondence: (J.T.C.); (J.L.N.)
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16
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Wang R, Reng M, Tian S, Liu C, Cheng H, Liu Y, Zhang H, Saqib M, Wei H, Wei Z. Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa. G3 (BETHESDA, MD.) 2021; 11:jkab195. [PMID: 34849817 PMCID: PMC8633455 DOI: 10.1093/g3journal/jkab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/29/2021] [Indexed: 01/15/2023]
Abstract
We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1727, 1723, and 1597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2639, and 2042 candidate target genes (CTGs) in the three respective stages of the same order. Correlation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS, and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis-related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in the dynamic regulation of secondary growth in woody tree species.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Mengxuan Reng
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Muhammad Saqib
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Hairong Wei
- College of Forest Resource and Environmental Science, Michigan Technological University, Houghton MI49931, USA
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
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17
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Ou Y, Kui H, Li J. Receptor-like Kinases in Root Development: Current Progress and Future Directions. MOLECULAR PLANT 2021; 14:166-185. [PMID: 33316466 DOI: 10.1016/j.molp.2020.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/17/2020] [Accepted: 12/09/2020] [Indexed: 05/11/2023]
Abstract
Cell-to-cell and cell-to-environment communications are critical to the growth and development of plants. Cell surface-localized receptor-like kinases (RLKs) are mainly involved in sensing various extracellular signals to initiate their corresponding cellular responses. As important vegetative organs for higher plants to adapt to a terrestrial living situation, roots play a critical role for the survival of plants. It has been demonstrated that RLKs control many biological processes during root growth and development. In this review, we summarize several key regulatory processes during Arabidopsis root development in which RLKs play critical roles. We also put forward a number of relevant questions that are required to be explored in future studies.
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Affiliation(s)
- Yang Ou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hong Kui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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18
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de Azevedo Manhães AME, Ortiz-Morea FA, He P, Shan L. Plant plasma membrane-resident receptors: Surveillance for infections and coordination for growth and development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:79-101. [PMID: 33305880 PMCID: PMC7855669 DOI: 10.1111/jipb.13051] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/08/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants are exposed to pathogen invasions and environmental fluctuations. To overcome the challenges of their surroundings, plants acquire the potential to sense endogenous and exogenous cues, resulting in their adaptability. Hence, plants have evolved a large collection of plasma membrane-resident receptors, including RECEPTOR-LIKE KINASEs (RLKs) and RECEPTOR-LIKE PROTEINs (RLPs) to perceive those signals and regulate plant growth, development, and immunity. The ability of RLKs and RLPs to recognize distinct ligands relies on diverse categories of extracellular domains evolved. Co-regulatory receptors are often required to associate with RLKs and RLPs to facilitate cellular signal transduction. RECEPTOR-LIKE CYTOPLASMIC KINASEs (RLCKs) also associate with the complex, bifurcating the signal to key signaling hubs, such as MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) cascades, to regulate diverse biological processes. Here, we discuss recent knowledge advances in understanding the roles of RLKs and RLPs in plant growth, development, and immunity, and their connection with co-regulatory receptors, leading to activation of diverse intracellular signaling pathways.
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Affiliation(s)
| | - Fausto Andres Ortiz-Morea
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Centro de Investigaciones Amazonicas CIMAZ-MACAGUAL, Universidad de la Amazonia, Florencia 180002622, Colombia
| | - Ping He
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Libo Shan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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19
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Wang Z, Gou X. Receptor-Like Protein Kinases Function Upstream of MAPKs in Regulating Plant Development. Int J Mol Sci 2020; 21:ijms21207638. [PMID: 33076465 PMCID: PMC7590044 DOI: 10.3390/ijms21207638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) are a group of protein kinase broadly involved in various signal pathways in eukaryotes. In plants, MAPK cascades regulate growth, development, stress responses and immunity by perceiving signals from the upstream regulators and transmitting the phosphorylation signals to the downstream signaling components. To reveal the interactions between MAPK cascades and their upstream regulators is important for understanding the functional mechanisms of MAPKs in the life span of higher plants. Typical receptor-like protein kinases (RLKs) are plasma membrane-located to perceive endogenous or exogenous signal molecules in regulating plant growth, development and immunity. MAPK cascades bridge the extracellular signals and intracellular transcription factors in many RLK-mediated signaling pathways. This review focuses on the current findings that RLKs regulate plant development through MAPK cascades and discusses questions that are worth investigating in the near future.
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