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Zhang Y, Wu W, Shen H, Yang L. Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis). BMC PLANT BIOLOGY 2024; 24:267. [PMID: 38600459 PMCID: PMC11005186 DOI: 10.1186/s12870-024-04827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/16/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND The Auxin Responsive Factor (ARF) family plays a crucial role in mediating auxin signal transduction and is vital for plant growth and development. However, the function of ARF genes in Korean pine (Pinus koraiensis), a conifer species of significant economic value, remains unclear. RESULTS This study utilized the whole genome of Korean pine to conduct bioinformatics analysis, resulting in the identification of 13 ARF genes. A phylogenetic analysis revealed that these 13 PkorARF genes can be classified into 4 subfamilies, indicating the presence of conserved structural characteristics within each subfamily. Protein interaction prediction indicated that Pkor01G00962.1 and Pkor07G00704.1 may have a significant role in regulating plant growth and development as core components of the PkorARFs family. Additionally, the analysis of RNA-seq and RT-qPCR expression patterns suggested that PkorARF genes play a crucial role in the development process of Korean pine. CONCLUSION Pkor01G00962.1 and Pkor07G00704.1, which are core genes of the PkorARFs family, play a potentially crucial role in regulating the fertilization and developmental process of Korean pine. This study provides a valuable reference for investigating the molecular mechanism of embryonic development in Korean pine and establishes a foundation for cultivating high-quality Korean pine.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wei Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Hailong Shen
- State Forestry and Grassland Administration Engineering Technology Research Center of Korean Pine, Harbin, 150040, China.
| | - Ling Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, 150040, China.
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2
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Xu L, Liu Y, Zhang J, Wu W, Hao Z, He S, Li Y, Shi J, Chen J. Genomic survey and expression analysis of LcARFs reveal multiple functions to somatic embryogenesis in Liriodendron. BMC PLANT BIOLOGY 2024; 24:94. [PMID: 38326748 PMCID: PMC10848544 DOI: 10.1186/s12870-024-04765-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND Auxin response factors (ARFs) are critical transcription factors that mediate the auxin signaling pathway and are essential for regulating plant growth. However, there is a lack of understanding regarding the ARF gene family in Liriodendron chinense, a vital species in landscaping and economics. Thus, further research is needed to explore the roles of ARFs in L. chinense and their potential applications in plant development. RESULT In this study, we have identified 20 LcARF genes that belong to three subfamilies in the genome of L. chinense. The analysis of their conserved domains, gene structure, and phylogeny suggests that LcARFs may be evolutionarily conserved and functionally similar to other plant ARFs. The expression of LcARFs varies in different tissues. Additionally, they are also involved in different developmental stages of somatic embryogenesis. Overexpression of LcARF1, LcARF2a, and LcARF5 led to increased activity within callus. Additionally, our promoter-GFP fusion study indicated that LcARF1 may play a role in embryogenesis. Overall, this study provides insights into the functions of LcARFs in plant development and embryogenesis, which could facilitate the improvement of somatic embryogenesis in L. chinense. CONCLUSION The research findings presented in this study shed light on the regulatory roles of LcARFs in somatic embryogenesis in L. chinense and may aid in accelerating the breeding process of this tree species. By identifying the specific LcARFs involved in different stages of somatic embryogenesis, this study provides a basis for developing targeted breeding strategies aimed at optimizing somatic embryogenesis in L. chinense, which holds great potential for improving the growth and productivity of this economically important species.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Ye Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Jiaji Zhang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Shichan He
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Yiran Li
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China.
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China.
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3
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Reddy VA, Saju JM, Nadimuthu K, Sarojam R. A non-canonical Aux/IAA gene MsIAA32 regulates peltate glandular trichome development in spearmint. FRONTIERS IN PLANT SCIENCE 2024; 15:1284125. [PMID: 38375083 PMCID: PMC10875047 DOI: 10.3389/fpls.2024.1284125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024]
Abstract
Phytohormone auxin controls various aspects of plant growth and development. The typical auxin signalling involves the degradation of canonical Aux/IAA proteins upon auxin perception releasing the auxin response factors (ARF) to activate auxin-regulated gene expression. Extensive research has been pursued in deciphering the role of canonical Aux/IAAs, however, the function of non-canonical Aux/IAA genes remains elusive. Here we identified a non-canonical Aux/IAA gene, MsIAA32 from spearmint (Mentha spicata), which lacks the TIR1-binding domain and shows its involvement in the development of peltate glandular trichomes (PGT), which are the sites for production and storage of commercially important essential oils. Using yeast two-hybrid studies, two canonical Aux/IAAs, MsIAA3, MsIAA4 and an ARF, MsARF3 were identified as the preferred binding partners of MsIAA32. Expression of a R2R3-MYB gene MsMYB36 and a cyclin gene MsCycB2-4 was altered in MsIAA32 suppressed plants indicating that these genes are possible downstream targets of MsIAA32 mediated signalling. Ectopic expression of MsIAA32 in Arabidopsis affected non-glandular trichome formation along with other auxin related developmental traits. Our findings establish the role of non-canonical Aux/IAA mediated auxin signalling in PGT development and reveal species-specific functionalization of Aux/IAAs.
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Affiliation(s)
| | | | | | - Rajani Sarojam
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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4
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Chen JJ, Wang W, Qin WQ, Men SZ, Li HL, Mitsuda N, Ohme-Takagi M, Wu AM. Transcription factors KNAT3 and KNAT4 are essential for integument and ovule formation in Arabidopsis. PLANT PHYSIOLOGY 2023; 191:463-478. [PMID: 36342216 PMCID: PMC9806662 DOI: 10.1093/plphys/kiac513] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Integuments form important protective cell layers surrounding the developing ovules in gymno- and angiosperms. Although several genes have been shown to influence the development of integuments, the transcriptional regulatory mechanism is still poorly understood. In this work, we report that the Class II KNOTTED1-LIKE HOMEOBOX (KNOX II) transcription factors KNOTTED1-LIKE HOMEBOX GENE 3 (KNAT3) and KNAT4 regulate integument development in Arabidopsis (Arabidopsis thaliana). KNAT3 and KNAT4 were co-expressed in inflorescences and especially in young developing ovules. The loss-of-function double mutant knat3 knat4 showed an infertility phenotype, in which both inner and outer integuments of the ovule are arrested at an early stage and form an amorphous structure as in the bell1 (bel1) mutant. The expression of chimeric KNAT3- and KNAT4-EAR motif repression domain (SRDX repressors) resulted in severe seed abortion. Protein-protein interaction assays demonstrated that KNAT3 and KNAT4 interact with each other and also with INNER NO OUTER (INO), a key transcription factor required for the outer integument formation. Transcriptome analysis showed that the expression of genes related with integument development is influenced in the knat3 knat4 mutant. The knat3 knat4 mutant also had a lower indole-3-acetic acid (IAA) content, and some auxin signaling pathway genes were downregulated. Moreover, transactivation analysis indicated that KNAT3/4 and INO activate the auxin signaling gene IAA INDUCIBLE 14 (IAA14). Taken together, our study identified KNAT3 and KNAT4 as key factors in integument development in Arabidopsis.
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Affiliation(s)
- Jia-Jun Chen
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wang
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå 90183, Sweden
| | - Wen-Qi Qin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Shu-Zhen Men
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hui-Ling Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Ai-Min Wu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
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5
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Kümpers BMC, Han J, Vaughan-Hirsch J, Redman N, Ware A, Atkinson JA, Leftley N, Janes G, Castiglione G, Tarr PT, Pyke K, Voß U, Wells DM, Bishopp A. Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy. PLANT PHYSIOLOGY 2022; 188:56-69. [PMID: 34718789 PMCID: PMC8774739 DOI: 10.1093/plphys/kiab503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Studying the developmental genetics of plant organs requires following gene expression in specific tissues. To facilitate this, we have developed dual expression anatomy lines, which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24 h. Coupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin.
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Affiliation(s)
- Britta M C Kümpers
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Jingyi Han
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Nicholas Redman
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Alexander Ware
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Nicola Leftley
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - George Janes
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | | | - Paul T Tarr
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
- Division of Biology and Biological Engineering 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Kevin Pyke
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Ute Voß
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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6
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Abstract
Auxin biology as a field has been at the forefront of advances in delineating the structures, dynamics, and control of plant growth networks. Advances have been enabled by combining the complementary fields of top-down, holistic systems biology and bottom-up, build-to-understand synthetic biology. Continued collaboration between these approaches will facilitate our understanding of and ability to engineer auxin's control of plant growth, development, and physiology. There is a need for the application of similar complementary approaches to improving equity and justice through analysis and redesign of the human systems in which this research is undertaken.
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Affiliation(s)
- R Clay Wright
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia 24061, USA
| | - Britney L Moss
- Department of Biology, Whitman College, Walla Walla, Washington 99362, USA
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7
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Gomes GLB, Scortecci KC. Auxin and its role in plant development: structure, signalling, regulation and response mechanisms. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:894-904. [PMID: 34396657 DOI: 10.1111/plb.13303] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/04/2021] [Indexed: 05/28/2023]
Abstract
Auxins are plant hormones that play a central role in controlling plant growth and development across different environmental conditions. Even at low concentrations, auxins can regulate gene expression through specific transcription factors and proteins that are modulated to environmental responses in the signalling cascade. Auxins are synthesized in tissues with high cell division activity and distributed by specific transmembrane proteins that regulate efflux and influx. This review presents recent advances in understanding the biosynthetic pathways, both dependent and independent of tryptophan, highlighting the intermediate indole compounds (indole-3-acetamide, indole-3-acetaldoxime, indole-3-pyruvic acid and tryptamine) and the key enzymes for auxin biosynthesis, such as YUCs and TAAs. In relation to the signalling cascade, it has been shown that auxins influence gene expression regulation by the connection between synthesis and distribution. Moreover, the molecular action of the auxin response factors and auxin/indole-3-acetic acid transcription factors with the F-box TIR1/AFB auxin receptors regulates gene expression. In addition, the importance of microRNAs in the auxin signalling pathway and their influence on plant plasticity to environmental fluctuations is also demonstrated. Finally, this review describes the chemical and biological processes involving auxins in plants.
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Affiliation(s)
- G L B Gomes
- Programa de Pós-Graduação em Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
- Laboratório de Transformação de Plantas e Análises em Microscopia, Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - K C Scortecci
- Programa de Pós-Graduação em Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
- Laboratório de Transformação de Plantas e Análises em Microscopia, Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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8
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Liu S, Wang C, Liu X, Navas-Castillo J, Zang L, Fan Z, Zhu X, Zhou T. Tomato chlorosis virus-encoded p22 suppresses auxin signalling to promote infection via interference with SKP1-Cullin-F-box TIR1 complex assembly. PLANT, CELL & ENVIRONMENT 2021; 44:3155-3172. [PMID: 34105183 DOI: 10.1111/pce.14125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 05/20/2023]
Abstract
Phytohormone auxin plays a fundamental role in plant growth and defense against pathogens. However, how auxin signalling is regulated during virus infection in plants remains largely unknown. Auxin/indole-3-acetic acid (Aux/IAA) is the repressor of auxin signalling and can be recognized by an F-box protein transport inhibitor response 1 (TIR1). Ubiquitination and degradation of Aux/IAA by SKP1-Cullin-F-boxTIR1 (SCFTIR1 ) complex can trigger auxin signalling. Here, with an emerging important plant virus worldwide, we showed that tomato chlorosis virus (ToCV) infection or stable transgenic overexpression of its p22 protein does not alter auxin accumulation level but significantly decreases the expression of auxin signalling-responsive genes, suggesting that p22 can attenuate host auxin signalling. Further, p22 could bind the C-terminal of SKP1.1 and compete with TIR1 to interfere with the SCFTIR1 complex assembly, leading to a suppression of Aux/IAA degradation. Silencing and over-expression assays suggested that both NbSKP1.1 and NbTIR1 suppress ToCV accumulation and disease symptoms. Altogether, ToCV p22 disrupts the auxin signalling through destabilizing SCFTIR1 by interacting with the C-terminal of NbSKP1.1 to promote ToCV infection. Our findings uncovered a previously unknown molecular mechanism employed by a plant virus to manipulate SCF complex-mediated ubiquitin pathway and to reprogram auxin signalling for efficient infection.
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Affiliation(s)
- Sijia Liu
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Cuilin Wang
- College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xuedong Liu
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas - Universidad de Málaga (IHSM-CSIC-UMA), Málaga, Spain
| | - Lianyi Zang
- College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xiaoping Zhu
- College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
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9
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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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10
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Saini S, Kaur N, Marothia D, Singh B, Singh V, Gantet P, Pati PK. Morphological Analysis, Protein Profiling and Expression Analysis of Auxin Homeostasis Genes of Roots of Two Contrasting Cultivars of Rice Provide Inputs on Mechanisms Involved in Rice Adaptation towards Salinity Stress. PLANTS 2021; 10:plants10081544. [PMID: 34451587 PMCID: PMC8399380 DOI: 10.3390/plants10081544] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/02/2021] [Accepted: 07/24/2021] [Indexed: 11/26/2022]
Abstract
Plants remodel their root architecture in response to a salinity stress stimulus. This process is regulated by an array of factors including phytohormones, particularly auxin. In the present study, in order to better understand the mechanisms involved in salinity stress adaptation in rice, we compared two contrasting rice cultivars—Luna Suvarna, a salt tolerant, and IR64, a salt sensitive cultivar. Phenotypic investigations suggested that Luna Suvarna in comparison with IR64 presented stress adaptive root traits which correlated with a higher accumulation of auxin in its roots. The expression level investigation of auxin signaling pathway genes revealed an increase in several auxin homeostasis genes transcript levels in Luna Suvarna compared with IR64 under salinity stress. Furthermore, protein profiling showed 18 proteins that were differentially regulated between the roots of two cultivars, and some of them were salinity stress responsive proteins found exclusively in the proteome of Luna Suvarna roots, revealing the critical role of these proteins in imparting salinity stress tolerance. This included proteins related to the salt overly sensitive pathway, root growth, the reactive oxygen species scavenging system, and abscisic acid activation. Taken together, our results highlight that Luna Suvarna involves a combination of morphological and molecular traits of the root system that could prime the plant to better tolerate salinity stress.
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Affiliation(s)
- Shivani Saini
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; (S.S.); (N.K.); (D.M.); (B.S.); (V.S.)
| | - Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; (S.S.); (N.K.); (D.M.); (B.S.); (V.S.)
| | - Deeksha Marothia
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; (S.S.); (N.K.); (D.M.); (B.S.); (V.S.)
| | - Baldev Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; (S.S.); (N.K.); (D.M.); (B.S.); (V.S.)
| | - Varinder Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; (S.S.); (N.K.); (D.M.); (B.S.); (V.S.)
| | - Pascal Gantet
- Université de Montpellier, UMR DIADE, Centre de Recherche de l’IRD, Avenue Agropolis, BP 64501, CEDEX 5, 34394 Montpellier, France
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Correspondence: (P.G.); (P.K.P.)
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; (S.S.); (N.K.); (D.M.); (B.S.); (V.S.)
- Correspondence: (P.G.); (P.K.P.)
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11
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Ramos Báez R, Nemhauser JL. Expansion and innovation in auxin signaling: where do we grow from here? Development 2021; 148:dev187120. [PMID: 33712444 PMCID: PMC7970066 DOI: 10.1242/dev.187120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phytohormone auxin plays a role in almost all growth and developmental responses. The primary mechanism of auxin action involves the regulation of transcription via a core signaling pathway comprising proteins belonging to three classes: receptors, co-receptor/co-repressors and transcription factors. Recent studies have revealed that auxin signaling can be traced back at least as far as the transition to land. Moreover, studies in flowering plants have highlighted how expansion of the gene families encoding auxin components is tied to functional diversification. As we review here, these studies paint a picture of auxin signaling evolution as a driver of innovation.
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Affiliation(s)
- Román Ramos Báez
- University of Washington, Department of Biology, Seattle, WA 98105-1800, USA
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12
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Perianez-Rodriguez J, Rodriguez M, Marconi M, Bustillo-Avendaño E, Wachsman G, Sanchez-Corrionero A, De Gernier H, Cabrera J, Perez-Garcia P, Gude I, Saez A, Serrano-Ron L, Beeckman T, Benfey PN, Rodríguez-Patón A, Del Pozo JC, Wabnik K, Moreno-Risueno MA. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis. SCIENCE ADVANCES 2021; 7:eabd4722. [PMID: 33523850 PMCID: PMC7775764 DOI: 10.1126/sciadv.abd4722] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/06/2020] [Indexed: 05/19/2023]
Abstract
In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.
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Affiliation(s)
- Juan Perianez-Rodriguez
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Marcos Rodriguez
- Departamento de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Marco Marconi
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Estefano Bustillo-Avendaño
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Guy Wachsman
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Hugues De Gernier
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Inmaculada Gude
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Laura Serrano-Ron
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Juan Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
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13
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Ishfaq M, Zhong Y, Wang Y, Li X. Magnesium Limitation Leads to Transcriptional Down-Tuning of Auxin Synthesis, Transport, and Signaling in the Tomato Root. FRONTIERS IN PLANT SCIENCE 2021; 12:802399. [PMID: 35003191 PMCID: PMC8733655 DOI: 10.3389/fpls.2021.802399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 05/08/2023]
Abstract
Magnesium (Mg) deficiency is becoming a widespread limiting factor for crop production. How crops adapt to Mg limitation remains largely unclear at the molecular level. Using hydroponic-cultured tomato seedlings, we found that total Mg2+ content significantly decreased by ∼80% under Mg limitation while K+ and Ca2+ concentrations increased. Phylogenetic analysis suggested that Mg transporters (MRS2/MGTs) constitute a previously uncharacterized 3-clade tree in planta with two rounds of asymmetric duplications, providing evolutionary evidence for further molecular investigation. In adaptation to internal Mg deficiency, the expression of six representative MGTs (two in the shoot and four in the root) was up-regulated in Mg-deficient plants. Contradictory to the transcriptional elevation of most of MGTs, Mg limitation resulted in the ∼50% smaller root system. Auxin concentrations particularly decreased by ∼23% in the Mg-deficient root, despite the enhanced accumulation of gibberellin, cytokinin, and ABA. In accordance with such auxin reduction was overall transcriptional down-regulation of thirteen genes controlling auxin biosynthesis (TAR/YUCs), transport (LAXs, PINs), and signaling (IAAs, ARFs). Together, systemic down-tuning of gene expression in the auxin signaling pathway under Mg limitation preconditions a smaller tomato root system, expectedly stimulating MGT transcription for Mg uptake or translocation.
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Affiliation(s)
- Muhammad Ishfaq
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Yanting Zhong
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
- Department of Vegetable Sciences, China Agricultural University, Beijing, China
| | - Yongqi Wang
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Xuexian Li
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
- *Correspondence: Xuexian Li,
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Maitra Majee S, Sharma E, Singh B, Khurana JP. Drought-induced protein (Di19-3) plays a role in auxin signaling by interacting with IAA14 in Arabidopsis. PLANT DIRECT 2020; 4:e00234. [PMID: 32582877 PMCID: PMC7306619 DOI: 10.1002/pld3.234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 05/08/2023]
Abstract
The members of early auxin response gene family, Aux/IAA, encode negative regulators of auxin signaling but play a central role in auxin-mediated plant development. Here we report the interaction of an Aux/IAA protein, AtIAA14, with Drought-induced-19 (Di19-3) protein and its possible role in auxin signaling. The Atdi19-3 mutant seedlings develop short hypocotyl, both in light and dark, and are compromised in temperature-induced hypocotyl elongation. The mutant plants accumulate more IAA and also show altered expression of NIT2, ILL5, and YUCCA genes involved in auxin biosynthesis and homeostasis, along with many auxin responsive genes like AUX1 and MYB77. Atdi19-3 seedlings show enhanced root growth inhibition when grown in the medium supplemented with auxin. Nevertheless, number of lateral roots is low in Atdi19-3 seedlings grown on the basal medium. We have shown that AtIAA14 physically interacts with AtDi19-3 in yeast two-hybrid (Y2H), bimolecular fluorescence complementation, and in vitro pull-down assays. However, the auxin-induced degradation of AtIAA14 in the Atdi19-3 seedlings was delayed. By expressing pIAA14::mIAA14-GFP in Atdi19-3 mutant background, it became apparent that both Di19-3 and AtIAA14 work in the same pathway and influence lateral root development in Arabidopsis. Gain-of-function slr-1/iaa14 (slr) mutant, like Atdi19-3, showed tolerance to abiotic stress in seed germination and cotyledon greening assays. The Atdi19-3 seedlings showed enhanced sensitivity to ethylene in triple response assay and AgNO3, an ethylene inhibitor, caused profuse lateral root formation in the mutant seedlings. These observations suggest that AtDi19-3 interacting with AtIAA14, in all probability, serves as a positive regulator of auxin signaling and also plays a role in some ethylene-mediated responses in Arabidopsis. SIGNIFICANCE STATEMENT This study has demonstrated interaction of auxin responsive Aux/IAA with Drought-induced 19 (Di19) protein and its possible implication in abiotic stress response.
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Affiliation(s)
- Susmita Maitra Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Brinderjit Singh
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Jitendra P. Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
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15
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Ramos Báez R, Buckley Y, Yu H, Chen Z, Gallavotti A, Nemhauser JL, Moss BL. A Synthetic Approach Allows Rapid Characterization of the Maize Nuclear Auxin Response Circuit. PLANT PHYSIOLOGY 2020; 182:1713-1722. [PMID: 32123041 PMCID: PMC7140906 DOI: 10.1104/pp.19.01475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/22/2020] [Indexed: 05/20/2023]
Abstract
Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis (Arabidopsis thaliana). Here, we used the nuclear Auxin Response Circuit recapitulated in yeast (Saccharomyces cerevisiae) system to functionally annotate maize (Zea mays) auxin signaling components, focusing on genes expressed during the development of ear and tassel inflorescences. All 16 maize auxin/indole-3-acetic acid repressor proteins were degraded in response to auxin with rates that depended on both receptor and repressor identities. When fused to the maize TOPLESS homolog RAMOSA1 ENHANCER LOCUS2, maize auxin/indole-3-acetic acids were able to repress AUXIN RESPONSE FACTOR transcriptional activity. A complete auxin response circuit comprising all maize components, including the ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was fully functional. The ZmAFB2/3 b1 auxin receptor was more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes.
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Affiliation(s)
- Román Ramos Báez
- University of Washington, Department of Biology, Seattle, Washington 98105
| | - Yuli Buckley
- Whitman College, Department of Biology, Walla Walla, Washington 99362
| | - Han Yu
- Whitman College, Department of Biology, Walla Walla, Washington 99362
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901
| | | | - Britney L Moss
- Whitman College, Department of Biology, Walla Walla, Washington 99362
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Guo Y, Wu Q, Xie Z, Yu B, Zeng R, Min Q, Huang J. OsFPFL4 is Involved in the Root and Flower Development by Affecting Auxin Levels and ROS Accumulation in Rice (Oryza sativa). RICE (NEW YORK, N.Y.) 2020; 13:2. [PMID: 31912314 PMCID: PMC6946790 DOI: 10.1186/s12284-019-0364-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/23/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND FPF1 (flowering-promoting factor 1) is one of the important family involved in the genetic control of flowering time in plant. Until now, limited knowledge concerning FPF1 family in rice has been understood. RESULTS As a homologue of AtFPF1, FPF1-like protein 4 of rice (OsFPFL4) is expressed in various tissues of plants. The functions of OsFPFL4 in rice were investigated by the reverse genetics approaches. Plants overexpressing OsFPFL4 have shorter primary root, more lateral roots and adventitious roots than wild type; however, RNA interference (RNAi) of OsFPFL4 significantly inhibits the growth of root system, and also delays the flowering time in rice. Interestingly, increased or repressed expression of OsFPFL4 leads to shrunken anthers and abnormal pollen grains. It is well recognized that auxin plays important roles in plant root and flower development, and the root elongation is also regulated by reactive oxygen species (ROS) homeostasis. Here, our results show that rice plants overexpressing OsFPFL4 accumulate more auxin in the shoot and root, whereas RNAi lines have less auxin than wild type. As expected, the transcript levels of genes responsible for auxin biosynthesis and polar transport are altered in these OsFPFL4 transgenic plants. As to ROS, slightly higher ROS levels were detected in overexpression root and inflorescence than the counterparts of wild type; however, the ROS levels were significantly increased in the RNAi lines, due to increased expression of ROS-producers and reduced expression of ROS-scavengers. CONCLUSION Our results reveal that OsFPFL4 is involved in modulating the root and flower development by affecting auxin and ROS homeostasis in rice plants. OsFPFL4 controls auxin accumulation via affecting auxin biosynthesis and transport, and also modulates ROS homeostasis by balancing ROS producing and scavenging. Thus, auxin-mediated ROS production might play a role in regulating redox status, which controls plant root and flower development.
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Affiliation(s)
- Yaomin Guo
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China
| | - Qi Wu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China
| | - Zizhao Xie
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China
| | | | - Rongfeng Zeng
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China
| | - Qian Min
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing, 400030, China.
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17
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Powers SK, Strader LC. Regulation of auxin transcriptional responses. Dev Dyn 2019; 249:483-495. [PMID: 31774605 PMCID: PMC7187202 DOI: 10.1002/dvdy.139] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/17/2019] [Accepted: 11/22/2019] [Indexed: 01/27/2023] Open
Abstract
The plant hormone auxin acts as a signaling molecule to regulate a vast number of developmental responses throughout all stages of plant growth. Tight control and coordination of auxin signaling is required for the generation of specific auxin‐response outputs. The nuclear auxin signaling pathway controls auxin‐responsive gene transcription through the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F‐BOX pathway. Recent work has uncovered important details into how regulation of auxin signaling components can generate unique and specific responses to determine auxin outputs. In this review, we discuss what is known about the core auxin signaling components and explore mechanisms important for regulating auxin response specificity. A review of recent updates to our understanding of auxin signaling.
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Affiliation(s)
- Samantha K Powers
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri
| | - Lucia C Strader
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri.,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri.,Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, Missouri
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18
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Abstract
Roots provide the primary mechanism that plants use to absorb water and nutrients from their environment. These functions are dependent on developmental mechanisms that direct root growth and branching into regions of soil where these resources are relatively abundant. Water is the most limiting factor for plant growth, and its availability is determined by the weather, soil structure, and salinity. In this review, we define the developmental pathways that regulate the direction of growth and branching pattern of the root system, which together determine the expanse of soil from which a plant can access water. The ability of plants to regulate development in response to the spatial distribution of water is a focus of many recent studies and provides a model for understanding how biological systems utilize positional cues to affect signaling and morphogenesis. A better understanding of these processes will inform approaches to improve crop water use efficiency to more sustainably feed a growing population.
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Affiliation(s)
- José R. Dinneny
- Department of Biology, Stanford University, Stanford, California 94305, USA
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19
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Hamm MO, Moss BL, Leydon AR, Gala HP, Lanctot A, Ramos R, Klaeser H, Lemmex AC, Zahler ML, Nemhauser JL, Wright RC. Accelerating structure-function mapping using the ViVa webtool to mine natural variation. PLANT DIRECT 2019; 3:e00147. [PMID: 31372596 PMCID: PMC6658840 DOI: 10.1002/pld3.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/20/2019] [Accepted: 04/29/2019] [Indexed: 05/13/2023]
Abstract
Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well-studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less-studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/).
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Affiliation(s)
- Morgan O. Hamm
- Department of BiologyUniversity of WashingtonSeattleWashington
| | | | | | - Hardik P. Gala
- Department of BiologyUniversity of WashingtonSeattleWashington
| | - Amy Lanctot
- Department of BiologyUniversity of WashingtonSeattleWashington
| | - Román Ramos
- Department of BiologyUniversity of WashingtonSeattleWashington
| | - Hannah Klaeser
- Department of BiologyWhitman CollegeWalla WallaWashington
| | | | | | | | - R. Clay Wright
- Biological Systems EngineeringVirginia TechBlacksburgVirginia
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20
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Wright RC, Nemhauser J. Plant Synthetic Biology: Quantifying the "Known Unknowns" and Discovering the "Unknown Unknowns". PLANT PHYSIOLOGY 2019; 179:885-893. [PMID: 30630870 PMCID: PMC6393784 DOI: 10.1104/pp.18.01222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 05/03/2023]
Abstract
Biosensors, advanced microscopy, and single- cell transcriptomics are advancing plant synthetic biology.
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Affiliation(s)
- R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia
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21
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Jing H, Strader LC. Interplay of Auxin and Cytokinin in Lateral Root Development. Int J Mol Sci 2019; 20:ijms20030486. [PMID: 30678102 PMCID: PMC6387363 DOI: 10.3390/ijms20030486] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 01/19/2023] Open
Abstract
The spacing and distribution of lateral roots are critical determinants of plant root system architecture. In addition to providing anchorage, lateral roots explore the soil to acquire water and nutrients. Over the past several decades, we have deepened our understanding of the regulatory mechanisms governing lateral root formation and development. In this review, we summarize these recent advances and provide an overview of how auxin and cytokinin coordinate the regulation of lateral root formation and development.
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Affiliation(s)
- Hongwei Jing
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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22
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Sun H, Xu F, Guo X, Wu D, Zhang X, Lou M, Luo F, Zhao Q, Xu G, Zhang Y. A Strigolactone Signal Inhibits Secondary Lateral Root Development in Rice. FRONTIERS IN PLANT SCIENCE 2019; 10:1527. [PMID: 31824543 PMCID: PMC6882917 DOI: 10.3389/fpls.2019.01527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/01/2019] [Indexed: 05/21/2023]
Abstract
Strigolactones (SLs) and their derivatives are plant hormones that have recently been identified as regulators of primary lateral root (LR) development. However, whether SLs mediate secondary LR production in rice (Oryza sativa L.), and how SLs and auxin interact in this process, remain unclear. In this study, the SL-deficient (dwarf10) and SL-insensitive (dwarf3) rice mutants and lines overexpressing OsPIN2 (OE) were used to investigate secondary LR development. The effects of exogenous GR24 (a synthetic SL analogue), 1-naphthylacetic acid (NAA; an exogenous auxin), 1-naphthylphthalamic acid (NPA; a polar auxin transport inhibitor), and abamine (a synthetic SL inhibitor) on rice secondary LR development were investigated. Rice d mutants with impaired SL biosynthesis and signaling exhibited increased secondary LR production compared with wild-type (WT) plants. Application of GR24 decreased the numbers of secondary LRs in dwarf10 (d10) plants but not in dwarf3 (d3), plants. These results indicate that SLs negatively regulate rice secondary LR production. Higher expression of DR5::GUS and more secondary LR primordia were found in the d mutants than in the WT plants. Exogenous NAA application increased expression of DR5::GUS in the WT, but had no effect on secondary LR formation. No secondary LRs were recorded in the OE lines, although DR5::GUS levels were higher than in the WT plants. However, on application of NPA, the numbers of secondary LRs were reduced in d10 and d3 mutants. Application of NAA increased the number of secondary LRs in the d mutants. GR24 eliminated the effect of NAA on secondary LR development in the d10, but not in the d3, mutants. These results demonstrate the importance of auxin in secondary LR formation, and that this process is inhibited by SLs via the D3 response pathway, but the interaction between auxin and SLs is complex.
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Affiliation(s)
- Huwei Sun
- Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Huwei Sun, ; Yali Zhang,
| | - Fugui Xu
- Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoli Guo
- Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Daxia Wu
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xuhong Zhang
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Manman Lou
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Feifei Luo
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Quanzhi Zhao
- Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Guohua Xu
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yali Zhang
- Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Huwei Sun, ; Yali Zhang,
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Tao S, Estelle M. Mutational studies of the Aux/IAA proteins in Physcomitrella reveal novel insights into their function. THE NEW PHYTOLOGIST 2018; 218:1534-1542. [PMID: 29461641 PMCID: PMC6054139 DOI: 10.1111/nph.15039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/09/2018] [Indexed: 05/27/2023]
Abstract
The plant hormone auxin regulates many aspects of plant growth and development. Auxin signaling involves hormone perception by the TRANSPORT INHIBITOR RESPONSE/AUXIN F-BOX (TIR1/AFB)-Aux/IAA co-receptor system, and the subsequent degradation of the Aux/IAA transcriptional repressors by the ubiquitin proteasome pathway. This leads to the activation of downstream gene expression and diverse physiological responses. Here, we investigate how the structural elements in the Aux/IAAs determine their function in Auxin perception and transcriptional repression. We took advantage of the facile genetics of the moss Physcomitrella patens to determine the activity of wild-type and mutant PpIAA1a proteins in a Δaux/iaa null background. In this way, Aux/IAA function was characterized at the molecular and physiological levels without the interference of genetic redundancy. We identified and characterized degron variants in Aux/IAAs that affect their stability and Auxin response. We also demonstrated that neither the Aux/IAA EAR motif nor Aux/IAA oligomerization is essential for the repressive function of Aux/IAA. Our study demonstrates how key elements within the Aux/IAA proteins fine tune stability and repressor activity, as well as the long-term developmental outcome.
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Affiliation(s)
- Sibo Tao
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark Estelle
- Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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24
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Luo J, Zhou JJ, Zhang JZ. Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function. Int J Mol Sci 2018; 19:ijms19010259. [PMID: 29337875 PMCID: PMC5796205 DOI: 10.3390/ijms19010259] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 12/31/2022] Open
Abstract
Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive genes, including the Auxin/Indole-3-Acetic Acid (Aux/IAA) family, the auxin response factor (ARF) family, small auxin upregulated RNA (SAUR), and the auxin-responsive Gretchen Hagen3 (GH3) family. Aux/IAA proteins are short-lived nuclear proteins comprising several highly conserved domains that are encoded by the auxin early response gene family. These proteins have specific domains that interact with ARFs and inhibit the transcription of genes activated by ARFs. Molecular studies have revealed that Aux/IAA family members can form diverse dimers with ARFs to regulate genes in various ways. Functional analyses of Aux/IAA family members have indicated that they have various roles in plant development, such as root development, shoot growth, and fruit ripening. In this review, recently discovered details regarding the molecular characteristics, regulation, and protein-protein interactions of the Aux/IAA proteins are discussed. These details provide new insights into the molecular basis of the Aux/IAA protein functions in plant developmental processes.
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Affiliation(s)
- Jie Luo
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing-Jing Zhou
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
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25
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Du Y, Scheres B. Lateral root formation and the multiple roles of auxin. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:155-167. [PMID: 28992266 DOI: 10.1093/jxb/erx223] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Root systems can display variable architectures that contribute to survival strategies of plants. The model plant Arabidopsis thaliana possesses a tap root system, in which the primary root and lateral roots (LRs) are major architectural determinants. The phytohormone auxin fulfils multiple roles throughout LR development. In this review, we summarize recent advances in our understanding of four aspects of LR formation: (i) LR positioning, which determines the spatial distribution of lateral root primordia (LRP) and LRs along primary roots; (ii) LR initiation, encompassing the activation of nuclear migration in specified lateral root founder cells (LRFCs) up to the first asymmetric cell division; (iii) LR outgrowth, the 'primordium-intrinsic' patterning of de novo organ tissues and a meristem; and (iv) LR emergence, an interaction between LRP and overlaying tissues to allow passage through cell layers. We discuss how auxin signaling, embedded in a changing developmental context, plays important roles in all four phases. In addition, we discuss how rapid progress in gene network identification and analysis, modeling, and four-dimensional imaging techniques have led to an increasingly detailed understanding of the dynamic regulatory networks that control LR development.
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Affiliation(s)
- Yujuan Du
- Plant Developmental Biology Group, Wageningen University Research, the Netherlands
| | - Ben Scheres
- Plant Developmental Biology Group, Wageningen University Research, the Netherlands
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26
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Kato H, Nishihama R, Weijers D, Kohchi T. Evolution of nuclear auxin signaling: lessons from genetic studies with basal land plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:291-301. [PMID: 28992186 DOI: 10.1093/jxb/erx267] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Auxin plays critical roles in growth and development through the regulation of cell differentiation, cell expansion, and pattern formation. The auxin signal is mainly conveyed through a so-called nuclear auxin pathway involving the receptor TIR1/AFB, the transcriptional co-repressor AUX/IAA, and the transcription factor ARF with direct DNA-binding ability. Recent progress in sequence information and molecular genetics in basal plants has provided many insights into the evolutionary origin of the nuclear auxin pathway and its pleiotropic roles in land plant development. In this review, we summarize the latest knowledge of the nuclear auxin pathway gained from studies using basal plants, including charophycean green algae and two major model bryophytes, Marchantia polymorpha and Physcomitrella patens. In addition, we discuss the functional implication of the increase in genetic complexity of the nuclear auxin pathway during land plant evolution.
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Affiliation(s)
- Hirotaka Kato
- Laboratory of Biochemistry, Wageningen University, The Netherlands
| | | | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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27
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Kircher S, Schopfer P. The plant hormone auxin beats the time for oscillating, light-regulated lateral root induction. Development 2018; 145:dev.169839. [DOI: 10.1242/dev.169839] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/29/2018] [Indexed: 11/20/2022]
Abstract
The molecular mechanism underlying the periodic induction of lateral roots, a paradigmatic example of clock-driven organ formation in plant development, is presently a matter of ongoing, controversial debate. Here we provide experimental evidence that this clock is frequency-modulated by light and that auxin serves as a mediator for translating continuous light signals into discontinuous gene activation signals preceding the initiation of lateral roots in Arabidopsis seedlings. Based on this evidence, we propose a molecular model of an ultradian biological clock involving auxin-dependent degradation of an AUX/IAA-type transcription repressor as a flexible, frequency-controlling delay element. This model widens the bandwidth of biological clocks by adding a new type that allows the pace of organ formation to adapt to the changing environmental demands of the growing plant.
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Affiliation(s)
- Stefan Kircher
- Department of Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University, Schänzlestr. 1, D-79104-Freiburg, Germany
| | - Peter Schopfer
- Department of Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University, Schänzlestr. 1, D-79104-Freiburg, Germany
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28
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Abstract
Auxin triggers diverse responses in plants, and this is reflected in quantitative and qualitative diversity in the auxin signaling machinery.
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Affiliation(s)
- Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
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29
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Zeng C, Ding Z, Zhou F, Zhou Y, Yang R, Yang Z, Wang W, Peng M. The Discrepant and Similar Responses of Genome-Wide Transcriptional Profiles between Drought and Cold Stresses in Cassava. Int J Mol Sci 2017; 18:ijms18122668. [PMID: 29231846 PMCID: PMC5751270 DOI: 10.3390/ijms18122668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 11/16/2022] Open
Abstract
Background: Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods: To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq. Results: Many genes specifically and commonly responsive to cold and drought were revealed: genes related to basic cellular metabolism, tetrapyrrole synthesis, and brassinosteroid metabolism exclusively responded to cold; genes related to abiotic stress and ethylene metabolism exclusively responded to drought; and genes related to cell wall, photosynthesis, and carbohydrate metabolism, DNA synthesis/chromatic structure, abscisic acid and salicylic acid metabolism, and calcium signaling commonly responded to both cold and drought. Discussion: Combined with cold- and/or drought-responsive transcription factors, the regulatory networks responding to cold and drought in cassava were constructed. All these findings will improve our understanding of the specific and common responses to cold and drought in cassava, and shed light on genetic improvement of cold and drought tolerance in cassava.
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Affiliation(s)
- Changying Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Fang Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yufei Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Ruiju Yang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zi Yang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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30
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Chen Y, Yang Q, Sang S, Wei Z, Wang P. Rice Inositol Polyphosphate Kinase (OsIPK2) Directly Interacts with OsIAA11 to Regulate Lateral Root Formation. PLANT & CELL PHYSIOLOGY 2017; 58:1891-1900. [PMID: 29016933 DOI: 10.1093/pcp/pcx125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
The plant hormone auxin controls many aspects of plant growth and development by promoting the degradation of Auxin/Indole-3-acetic acid (Aux/IAA) proteins. The domain II (DII) of Aux/IAA proteins is sufficient for eliciting the degradation by directly interacting with the auxin receptor F-box protein TIR1 to form a TIR1/AFBs-Aux/IAA complex in an auxin-dependent manner. However, the underlying mechanisms of fine-tuning Aux/IAA degradation by auxin stimuli remain to be elucidated. Here, we show that OsIPK2, a rice (Oryza sativa) inositol polyphosphate kinase, directly interacts with an Aux/IAA protein OsIAA11 to repress its degradation. In a rice protoplast transient expression system, the auxin-induced degradation of Myc-OsIAA11 fusion was delayed by co-expressed GFP-OsIPK2 proteins. Furthermore, expressing additional OsIPK2 or its N-terminal amino acid sequence enhanced the accumulation of OsIAA11 proteins in transgenic plants, which in turn caused defects in lateral root formation and auxin response. Taken together, we identify a novel co-factor of Aux/IAA in auxin signaling and demonstrate its role in regulating lateral root development.
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Affiliation(s)
- Yao Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Qiaofeng Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Sihong Sang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhaoyun Wei
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Peng Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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31
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Wright RC, Zahler ML, Gerben SR, Nemhauser JL. Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants. Genetics 2017; 207:583-591. [PMID: 28760746 PMCID: PMC5629325 DOI: 10.1534/genetics.117.300092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/24/2017] [Indexed: 12/20/2022] Open
Abstract
The evolution of complex body plans in land plants has been paralleled by gene duplication and divergence within nuclear auxin-signaling networks. A deep mechanistic understanding of auxin signaling proteins therefore may allow rational engineering of novel plant architectures. Toward that end, we analyzed natural variation in the auxin receptor F-box family of wild accessions of the reference plant Arabidopsis thaliana and used this information to populate a structure/function map. We employed a synthetic assay to identify natural hypermorphic F-box variants and then assayed auxin-associated phenotypes in accessions expressing these variants. To more directly measure the impact of the strongest variant in our synthetic assay on auxin sensitivity, we generated transgenic plants expressing this allele. Together, our findings link evolved sequence variation to altered molecular performance and auxin sensitivity. This approach demonstrates the potential for combining synthetic biology approaches with quantitative phenotypes to harness the wealth of available sequence information and guide future engineering efforts of diverse signaling pathways.
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Affiliation(s)
- R Clay Wright
- Department of Biology, University of Washington, Seattle, Washington 98195-1800
| | - Mollye L Zahler
- Department of Biology, University of Washington, Seattle, Washington 98195-1800
| | - Stacey R Gerben
- Department of Biology, University of Washington, Seattle, Washington 98195-1800
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32
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Roy Choudhury S, Pandey S. Recently duplicated plant heterotrimeric Gα proteins with subtle biochemical differences influence specific outcomes of signal-response coupling. J Biol Chem 2017; 292:16188-16198. [PMID: 28827312 PMCID: PMC5625049 DOI: 10.1074/jbc.m117.793380] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/10/2017] [Indexed: 12/31/2022] Open
Abstract
Heterotrimeric G-proteins, comprising Gα, Gβ, and Gγ subunits, regulate key signaling processes in eukaryotes. The Gα subunit determines the status of signaling by switching between inactive GDP-bound and active GTP-bound forms. Unlike animal systems, in which multiple Gα proteins with variable biochemical properties exist, plants have fewer, highly similar Gα subunits that have resulted from recent genome duplications. These proteins exhibit subtle differences in their GTP-binding, GDP/GTP-exchange, and GTP-hydrolysis activities, but the extent to which these differences contribute to affect plant signaling and development remains unknown. To evaluate this, we expressed native and engineered Gα proteins from soybean in an Arabidopsis Gα-null background and studied their effects on modulating a range of developmental and hormonal signaling phenotypes. Our results indicated that inherent biochemical differences in these highly similar Gα proteins are biologically relevant, and some proteins are more flexible than others in influencing the outcomes of specific signals. These observations suggest that alterations in the rate of the G-protein cycle itself may contribute to the specificity of response regulation in plants by affecting the duration of active signaling and/or by the formation of distinct protein-protein complexes. In species such as Arabidopsis having a single canonical Gα, this rate could be affected by regulatory proteins in the presence of specific signals, whereas in plants with multiple Gα proteins, an even more complex regulation may exist, which likely contributes to the specificity of signal-response coupling.
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Affiliation(s)
| | - Sona Pandey
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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33
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Brophy JAN, LaRue T, Dinneny JR. Understanding and engineering plant form. Semin Cell Dev Biol 2017; 79:68-77. [PMID: 28864344 DOI: 10.1016/j.semcdb.2017.08.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022]
Abstract
A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.
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Affiliation(s)
- Jennifer A N Brophy
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Therese LaRue
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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34
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Mironova V, Teale W, Shahriari M, Dawson J, Palme K. The Systems Biology of Auxin in Developing Embryos. TRENDS IN PLANT SCIENCE 2017; 22:225-235. [PMID: 28131745 DOI: 10.1016/j.tplants.2016.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 05/13/2023]
Abstract
Systems biology orientates signaling pathways in their biological context. This aim invariably requires models that ignore extraneous factors and focus on the most crucial pathways of any given process. The developing embryo encapsulates many important processes in plant development; understanding their interaction will be key to designing crops able to maximize yield in an ever-more challenging world. Here, we briefly summarize the role of auxin during embryo development. We highlight recent advances in our understanding of auxin signaling and discuss implications for a systems understanding of development.
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Affiliation(s)
- Victoria Mironova
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - William Teale
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Mojgan Shahriari
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Jonathan Dawson
- Department of Physics, Syracuse University, Syracuse, NY 13210, USA
| | - Klaus Palme
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Freiburg 79104, Germany; Freiburg Institute of Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, Freiburg79104, Germany.
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35
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Functional analysis of molecular interactions in synthetic auxin response circuits. Proc Natl Acad Sci U S A 2016; 113:11354-11359. [PMID: 27647902 DOI: 10.1073/pnas.1604379113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Auxin-regulated transcription pivots on the interaction between the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressor proteins and the AUXIN RESPONSE FACTOR (ARF) transcription factors. Recent structural analyses of ARFs and Aux/IAAs have raised questions about the functional complexes driving auxin transcriptional responses. To parse the nature and significance of ARF-DNA and ARF-Aux/IAA interactions, we analyzed structure-guided variants of synthetic auxin response circuits in the budding yeast Saccharomyces cerevisiae Our analysis revealed that promoter architecture could specify ARF activity and that ARF19 required dimerization at two distinct domains for full transcriptional activation. In addition, monomeric Aux/IAAs were able to repress ARF activity in both yeast and plants. This systematic, quantitative structure-function analysis identified a minimal complex-comprising a single Aux/IAA repressing a pair of dimerized ARFs-sufficient for auxin-induced transcription.
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36
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Guseman JM, Nemhauser JL, Moss BL. A Live-imaging, Heat Shock-inducible System to Measure Aux/IAA Degradation Rates in Planta. Bio Protoc 2016; 6:e1881. [PMID: 29725609 DOI: 10.21769/bioprotoc.1881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
An emerging theme in biology is the importance of cellular signaling dynamics. In addition to monitoring changes in absolute abundance of signaling molecules, many signal transduction pathways are sensitive to changes in temporal properties of signaling components (Purvis and Lahav, 2013). The phytohormone auxin regulates myriad processes in plant development. Many of these require the nuclear auxin signaling pathway, in which degradation of the Aux/IAA repressor proteins allows for transcription of auxin-responsive genes (Korasick et al., 2015). Using a heterologous yeast system, we found that Aux/IAAs exhibit a range of auxin-induced degradation rates when co-expressed in isolation with F-box proteins (Havens et al., 2012). Subsequent studies connecting signaling dynamics to plant growth and development confirmed that Aux/IAAs show similar differences in plants (Guseman et al., 2015; Moss et al., 2015). Here, we describe in detail the use of a heat-shock-inducible fluorescence degradation system to capture Aux/IAA degradation in real time in live plant roots. By employing this method, we were able to obtain high Aux/IAA expression and avoid the dampening long term effects of turnover, feedback and silencing. Degradation was dependent on the presence of an Aux/IAA degron and rates increased in response to exogenous auxin.
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Affiliation(s)
- Jessica M Guseman
- Department of Biology, University of Washington, Seattle, WA, USA.,USDA Appalachian Fruit Research, Kearneysville, WV, USA
| | | | - Britney L Moss
- Department of Biology, University of Washington, Seattle, WA, USA.,Department of Biology & Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, WA, USA
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37
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Zhou C, Guo J, Zhu L, Xiao X, Xie Y, Zhu J, Ma Z, Wang J. Paenibacillus polymyxa BFKC01 enhances plant iron absorption via improved root systems and activated iron acquisition mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 105:162-173. [PMID: 27105423 DOI: 10.1016/j.plaphy.2016.04.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 04/13/2016] [Accepted: 04/14/2016] [Indexed: 05/19/2023]
Abstract
Despite the high abundance of iron (Fe) in most earth's soils, Fe is the major limiting factor for plant growth and development due to its low bioavailability. With an increasing recognition that soil microbes play important roles in plant growth, several strains of beneficial rhizobactria have been applied to improve plant nutrient absorption, biomass, and abiotic or biotic stress tolerance. In this study, we report the mechanisms of microbe-induced plant Fe assimilation, in which the plant growth promoting rhizobacteria (PGPR) Paenibacillus polymyxa BFKC01 stimulates plant's Fe acquisition machinery to enhance Fe uptake in Arabidopsis plants. Mechanistic studies show that BFKC01 transcriptionally activates the Fe-deficiency-induced transcription factor 1 (FIT1), thereby up-regulating the expression of IRT1 and FRO2. Furthermore, BFKC01 has been found to induce plant systemic responses with the increased transcription of MYB72, and the biosynthetic pathways of phenolic compounds are also activated. Our data reveal that abundant phenolic compounds are detected in root exudation of the BFKC01-inoculated plants, which efficiently facilitate Fe mobility under alkaline conditions. In addition, BFKC01 can secret auxin and further improved root systems, which enhances the ability of plants to acquire Fe from soils. As a result, BFKC01-inoculated plants have more endogenous Fe and increased photosynthetic capacity under alkaline conditions as compared to control plants. Our results demonstrate the potential roles of BFKC01 in promoting Fe acquisition in plants and underline the intricate integration of microbial signaling in controlling plant Fe acquisition.
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Affiliation(s)
- Cheng Zhou
- Key Laboratory of Bio-organic Fertilizer Creation, Ministry of Agriculture, Institute for Applied Microbiology, Anhui Science and Technology University, Bengbu 233100, China
| | - Jiansheng Guo
- School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Lin Zhu
- Department of Molecular and Cell Biology, Tongji University, Shanghai 200092, China
| | - Xin Xiao
- Key Laboratory of Bio-organic Fertilizer Creation, Ministry of Agriculture, Institute for Applied Microbiology, Anhui Science and Technology University, Bengbu 233100, China
| | - Yue Xie
- Key Laboratory of Bio-organic Fertilizer Creation, Ministry of Agriculture, Institute for Applied Microbiology, Anhui Science and Technology University, Bengbu 233100, China
| | - Jian Zhu
- Department of Molecular and Cell Biology, Tongji University, Shanghai 200092, China
| | - Zhongyou Ma
- Key Laboratory of Bio-organic Fertilizer Creation, Ministry of Agriculture, Institute for Applied Microbiology, Anhui Science and Technology University, Bengbu 233100, China.
| | - Jianfei Wang
- Key Laboratory of Bio-organic Fertilizer Creation, Ministry of Agriculture, Institute for Applied Microbiology, Anhui Science and Technology University, Bengbu 233100, China.
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38
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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Abstract
Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.
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Affiliation(s)
- Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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40
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Zhou S, Okekeogbu I, Sangireddy S, Ye Z, Li H, Bhatti S, Hui D, McDonald DW, Yang Y, Giri S, Howe KJ, Fish T, Thannhauser TW. Proteome Modification in Tomato Plants upon Long-Term Aluminum Treatment. J Proteome Res 2016; 15:1670-84. [DOI: 10.1021/acs.jproteome.6b00128] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Suping Zhou
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Ikenna Okekeogbu
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Sasikiran Sangireddy
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Zhujia Ye
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Hui Li
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Sarabjit Bhatti
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Dafeng Hui
- Department
of Agricultural and Environmental Sciences, College of Agriculture,
Human and Natural Sciences, Tennessee State University, 3500 John
A Merritt Blvd, Nashville, Tennessee 37209, United States
| | - Daniel W. McDonald
- Phenotype Screening Corporation, 4028 Papermill Road, Knoxville, Tennessee 37909, United States
| | - Yong Yang
- RW Holley
Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA-ARS, Tower Rd, Ithaca, New York 14853, United States
| | - Shree Giri
- RW Holley
Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA-ARS, Tower Rd, Ithaca, New York 14853, United States
| | - Kevin J. Howe
- RW Holley
Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA-ARS, Tower Rd, Ithaca, New York 14853, United States
| | - Tara Fish
- RW Holley
Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA-ARS, Tower Rd, Ithaca, New York 14853, United States
| | - Theodore W. Thannhauser
- RW Holley
Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA-ARS, Tower Rd, Ithaca, New York 14853, United States
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41
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Dinesh DC, Villalobos LIAC, Abel S. Structural Biology of Nuclear Auxin Action. TRENDS IN PLANT SCIENCE 2016; 21:302-316. [PMID: 26651917 DOI: 10.1016/j.tplants.2015.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 05/23/2023]
Abstract
Auxin coordinates plant development largely via hierarchical control of gene expression. During the past decades, the study of early auxin genes paired with the power of Arabidopsis genetics have unraveled key nuclear components and molecular interactions that perceive the hormone and activate primary response genes. Recent research in the realm of structural biology allowed unprecedented insight into: (i) the recognition of auxin-responsive DNA elements by auxin transcription factors; (ii) the inactivation of those auxin response factors by early auxin-inducible repressors; and (iii) the activation of target genes by auxin-triggered repressor degradation. The biophysical studies reviewed here provide an impetus for elucidating the molecular determinants of the intricate interactions between core components of the nuclear auxin response module.
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Affiliation(s)
- Dhurvas Chandrasekaran Dinesh
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Luz Irina A Calderón Villalobos
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany; Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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42
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Taylor-Teeples M, Lanctot A, Nemhauser JL. As above, so below: Auxin's role in lateral organ development. Dev Biol 2016; 419:156-164. [PMID: 26994944 DOI: 10.1016/j.ydbio.2016.03.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 02/02/2023]
Abstract
Organogenesis requires the coordination of many highly-regulated developmental processes, including cell fate determination, cell division and growth, and cell-cell communication. For tissue- and organ-scale coordination, a network of regulators enables molecular events in individual cells to translate into multicellular changes in structure and functional capacity. One recurrent theme in plant developmental networks is a central role for plant hormones, especially auxin. Here, we focus first on describing recent advances in understanding lateral root development, one of the best-studied examples of auxin-mediated organogenesis. We then use this framework to examine the parallel process of emergence of lateral organs in the shoot-a process called phyllotaxy. This comparison reveals a high degree of conservation, highlighting auxin's pivotal role determining overall plant architecture.
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Affiliation(s)
| | - Amy Lanctot
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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43
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Nemhauser JL, Torii KU. Plant synthetic biology for molecular engineering of signalling and development. NATURE PLANTS 2016; 2:16010. [PMID: 27249346 PMCID: PMC5164986 DOI: 10.1038/nplants.2016.10] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.
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Affiliation(s)
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
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44
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Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. THE NEW PHYTOLOGIST 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
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45
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Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K. It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana. THE PLANT CELL 2016; 28:6-16. [PMID: 26744219 PMCID: PMC4746685 DOI: 10.1105/tpc.15.00878] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/11/2015] [Accepted: 01/07/2016] [Indexed: 05/19/2023]
Abstract
Ubiquitination, the covalent binding of the small protein modifier ubiquitin to a target protein, is an important and frequently studied posttranslational protein modification. Multiple reports provide useful insights into the plant ubiquitinome, but mostly at the protein level without comprehensive site identification. Here, we implemented ubiquitin combined fractional diagonal chromatography (COFRADIC) for proteome-wide ubiquitination site mapping on Arabidopsis thaliana cell cultures. We identified 3009 sites on 1607 proteins, thereby greatly increasing the number of known ubiquitination sites in this model plant. Finally, The Ubiquitination Site tool (http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/) gives access to the obtained ubiquitination sites, not only to consult the ubiquitination status of a given protein, but also to conduct intricate experiments aiming to study the roles of specific ubiquitination events. Together with the antibodies recognizing the ubiquitin remnant motif, ubiquitin COFRADIC represents a powerful tool to resolve the ubiquitination maps of numerous cellular processes in plants.
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Affiliation(s)
- Alan Walton
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Nicolas Cybulski
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sabrina Iñigo
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Evy Timmerman
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Jefri Heyman
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
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46
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Auxin signaling modules regulate maize inflorescence architecture. Proc Natl Acad Sci U S A 2015; 112:13372-7. [PMID: 26464512 DOI: 10.1073/pnas.1516473112] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plants, small groups of pluripotent stem cells called axillary meristems are required for the formation of the branches and flowers that eventually establish shoot architecture and drive reproductive success. To ensure the proper formation of new axillary meristems, the specification of boundary regions is required for coordinating their development. We have identified two maize genes, BARREN INFLORESCENCE1 and BARREN INFLORESCENCE4 (BIF1 and BIF4), that regulate the early steps required for inflorescence formation. BIF1 and BIF4 encode AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins, which are key components of the auxin hormone signaling pathway that is essential for organogenesis. Here we show that BIF1 and BIF4 are integral to auxin signaling modules that dynamically regulate the expression of BARREN STALK1 (BA1), a basic helix-loop-helix (bHLH) transcriptional regulator necessary for axillary meristem formation that shows a striking boundary expression pattern. These findings suggest that auxin signaling directly controls boundary domains during axillary meristem formation and define a fundamental mechanism that regulates inflorescence architecture in one of the most widely grown crop species.
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47
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Lavedrine C, Farcot E, Vernoux T. Modeling plant development: from signals to gene networks. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:148-153. [PMID: 26247125 DOI: 10.1016/j.pbi.2015.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/29/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
Mathematical modeling has become a common tool in plant developmental biology. Indeed, it allows for the prediction of complex and often unintuitive dynamics of the molecular networks driving plant development. This has enabled the test of their possible involvement in robust and specific developmental processes. Modeling has also been fruitful in predicting new interactions within gene networks, such as the Arabidopsis circadian clock. A new challenge is to integrate patterning issues with tissue growth and biomechanics. The development of new tools to gain resolution in data collection as well as new frameworks to confront models and data might provide even more robust predictions.
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Affiliation(s)
- Cyril Lavedrine
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Etienne Farcot
- School of Mathematical Sciences & Centre for Plant Integrative Biology, University of Nottingham, NG7 2RD, United Kingdom.
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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48
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Moss BL, Mao H, Guseman JM, Hinds TR, Hellmuth A, Kovenock M, Noorassa A, Lanctot A, Villalobos LIAC, Zheng N, Nemhauser JL. Rate Motifs Tune Auxin/Indole-3-Acetic Acid Degradation Dynamics. PLANT PHYSIOLOGY 2015; 169:803-13. [PMID: 26149575 PMCID: PMC4577399 DOI: 10.1104/pp.15.00587] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/03/2015] [Indexed: 05/19/2023]
Abstract
Ubiquitin-mediated protein degradation is a common feature in diverse plant cell signaling pathways; however, the factors that control the dynamics of regulated protein turnover are largely unknown. One of the best-characterized families of E3 ubiquitin ligases facilitates ubiquitination of auxin (aux)/indole-3-acetic acid (IAA) repressor proteins in the presence of auxin. Rates of auxin-induced degradation vary widely within the Aux/IAA family, and sequences outside of the characterized degron (the minimum region required for auxin-induced degradation) can accelerate or decelerate degradation. We have used synthetic auxin degradation assays in yeast (Saccharomyces cerevisiae) and in plants to characterize motifs flanking the degron that contribute to tuning the dynamics of Aux/IAA degradation. The presence of these rate motifs is conserved in phylogenetically distant members of the Arabidopsis (Arabidopsis thaliana) Aux/IAA family, as well as in their putative Brassica rapa orthologs. We found that rate motifs can act by enhancing interaction between repressors and the E3, but that this is not the only mechanism of action. Phenotypes of transgenic plants expressing a deletion in a rate motif in IAA28 resembled plants expressing degron mutations, underscoring the functional relevance of Aux/IAA degradation dynamics in regulating auxin responses.
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Affiliation(s)
- Britney L Moss
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Haibin Mao
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Jessica M Guseman
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Thomas R Hinds
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Antje Hellmuth
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Marlies Kovenock
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Anisa Noorassa
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Amy Lanctot
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Luz Irina A Calderón Villalobos
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Ning Zheng
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
| | - Jennifer L Nemhauser
- Departments of Biology (B.L.M., J.M.G., M.K., A.N., A.L., J.L.N.) and Pharmacology (H.M., T.R.H., N.Z.), University of Washington, Seattle, Washington 98195;Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (A.H., L.I.A.C.V.); andHoward Hughes Medical Institute, Chevy Chase, Maryland 20815 (N.Z.)
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The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nat Commun 2015; 6:7641. [PMID: 26144255 DOI: 10.1038/ncomms8641] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/27/2015] [Indexed: 01/05/2023] Open
Abstract
The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence.
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Guseman JM, Hellmuth A, Lanctot A, Feldman TP, Moss BL, Klavins E, Calderón Villalobos LIA, Nemhauser JL. Auxin-induced degradation dynamics set the pace for lateral root development. J Cell Sci 2015. [DOI: 10.1242/jcs.170464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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