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Rong M, Gao SX, Wen D, Xu YH, Wei JH. The LOB domain protein, a novel transcription factor with multiple functions: A review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108922. [PMID: 39038384 DOI: 10.1016/j.plaphy.2024.108922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024]
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein, named for its LATERAL ORGAN BOUNDARIES (LOB) domain, is a member of a class of specific transcription factors commonly found in plants and is absent from all other groups of organisms. LBD TFs have been systematically identified in about 35 plant species and are involved in regulating various aspects of plant growth and development. However, research on the signaling network and regulatory functions of LBD TFs is insufficient, and only a few members have been studied. Moreover, a comprehensive review of these existing studies is lacking. In this review, the structure, regulatory mechanism and function of LBD TFs in recent years were reviewed in order to better understand the role of LBD TFs in plant growth and development, and to provide a new perspective for the follow-up study of LBD TFs.
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Affiliation(s)
- Mei Rong
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Shi-Xi Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Dong Wen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yan-Hong Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Jian-He Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, 570311, China.
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2
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Zhang F, Wang J, Ding T, Lin X, Hu H, Ding Z, Tian H. MYB2 and MYB108 regulate lateral root development by interacting with LBD29 in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1675-1687. [PMID: 38923126 DOI: 10.1111/jipb.13720] [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: 03/24/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024]
Abstract
AUXIN RESPONSE FACTOR 7 (ARF7)-mediated auxin signaling plays a key role in lateral root (LR) development by regulating downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor genes, including LBD16, LBD18, and LBD29. LBD proteins are believed to regulate the transcription of downstream genes as homodimers or heterodimers. However, whether LBD29 forms dimers with other proteins to regulate LR development remains unknown. Here, we determined that the Arabidopsis thaliana (L.) Heynh. MYB transcription factors MYB2 and MYB108 interact with LBD29 and regulate auxin-induced LR development. Both MYB2 and MYB108 were induced by auxin in an ARF7-dependent manner. Disruption of MYB2 by fusion with an SRDX domain severely affected auxin-induced LR formation and the ability of LBD29 to induce LR development. By contrast, overexpression of MYB2 or MYB108 resulted in greater LR numbers, except in the lbd29 mutant background. These findings underscore the interdependence and importance of MYB2, MYB108, and LBD29 in regulating LR development. In addition, MYB2-LBD29 and MYB108-LBD29 complexes promoted the expression of CUTICLE DESTRUCTING FACTOR 1 (CDEF1), a member of the GDSL (Gly-Asp-Ser-Leu) lipase/esterase family involved in LR development. In summary, this study identified MYB2-LBD29 and MYB108-LBD29 regulatory modules that act downstream of ARF7 and intricately control auxin-mediated LR development.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Junxia Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Tingting Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xuefeng Lin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Haiying Hu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Huiyu Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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Lin S, Medina CA, Wang G, Combs D, Shewmaker G, Fransen S, Llewellyn D, Norberg S, Yu LX. Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:121. [PMID: 37119337 DOI: 10.1007/s00122-023-04364-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
The use of multi-environment trials to test yield-related traits in a diverse alfalfa panel allowed to find multiple molecular markers associated with complex agronomic traits. Yield is one of the most important target traits in alfalfa breeding; however, yield is a complex trait affected by genetic and environmental factors. In this study, we used multi-environment trials to test yield-related traits in a diverse panel composed of 200 alfalfa accessions and varieties. Phenotypic data of maturity stage measured as mean stage by count (MSC), dry matter content, plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. Single-trial and stagewise analyses were used to obtain estimated trait means of entries by environment. The plants were genotyped using a genotyping by sequencing approach and obtained a genotypic matrix with 97,345 single nucleotide polymorphisms. Genome-wide association studies identified a total of 84 markers associated with the traits analyzed. Of those, 29 markers were in noncoding regions and 55 markers were in coding regions. Ten significant SNPs at the same locus were associated with FD and they were linked to a gene annotated as a nuclear fusion defective 4-like (NFD4). Additional SNPs associated with MSC, PH, and Yi were annotated as transcription factors such as Cysteine3Histidine (C3H), Hap3/NF-YB family, and serine/threonine-protein phosphatase 7 proteins, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed up the genetic gain toward alfalfa yield improvement.
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Affiliation(s)
- Sen Lin
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
| | - Cesar A Medina
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
| | - Guojie Wang
- Department of Crop and Soil Science, Oregon State University, LaGrande, OR, USA
| | - David Combs
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Steve Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Don Llewellyn
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Steven Norberg
- Franklin County Extension Office, Washington State University, Pasco, WA, USA.
| | - Long-Xi Yu
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA.
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4
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Li Y, Zhang Y, Li B, Hou L, Yu J, Jia C, Wang Z, Chen S, Zhang M, Qin J, Cao N, Cui J, Shi W. Preliminary Expression Analysis of the OSCA Gene Family in Maize and Their Involvement in Temperature Stress. Int J Mol Sci 2022; 23:13658. [PMID: 36362446 PMCID: PMC9656168 DOI: 10.3390/ijms232113658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/05/2022] [Indexed: 12/01/2023] Open
Abstract
Hyperosmolality-gated calcium-permeable channels (OSCA) are characterized as an osmosensor in plants; they are able to recognize and respond to exogenous and endogenous osmotic changes, and play a vital role in plant growth and adaptability to environmental stress. To explore the potential biological functions of OSCAs in maize, we performed a bioinformatics and expression analysis of the ZmOSCA gene family. Using bioinformatics methods, we identified twelve OSCA genes from the genome database of maize. According to their sequence composition and phylogenetic relationship, the maize OSCA family was classified into four groups (Ⅰ, Ⅱ, Ⅲ, and Ⅳ). Multiple sequence alignment analysis revealed a conserved DUF221 domain in these members. We modeled the calcium binding sites of four OSCA families using the autodocking technique. The expression profiles of ZmOSCA genes were analyzed in different tissues and under diverse abiotic stresses such as drought, salt, high temperature, and chilling using quantitative real-time PCR (qRT-PCR). We found that the expression of twelve ZmOSCA genes is variant in different tissues of maize. Furthermore, abiotic stresses such as drought, salt, high temperature, and chilling differentially induced the expression of twelve ZmOSCA genes. We chose ZmOSCA2.2 and ZmOSCA2.3, which responded most strongly to temperature stress, for prediction of protein interactions. We modeled the calcium binding sites of four OSCA families using autodocking tools, obtaining a number of new results. These results are helpful in understanding the function of the plant OSCA gene family for study of the molecular mechanism of plant osmotic stress and response, as well as exploration of the interaction between osmotic stress, high-temperature stress, and low-temperature stress signal transduction mechanisms. As such, they can provide a theoretical basis for crop breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Wuliang Shi
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun 130062, China
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Zhang F, Tao W, Sun R, Wang J, Li C, Kong X, Tian H, Ding Z. PRH1 mediates ARF7-LBD dependent auxin signaling to regulate lateral root development in Arabidopsis thaliana. PLoS Genet 2020; 16:e1008044. [PMID: 32032352 PMCID: PMC7006904 DOI: 10.1371/journal.pgen.1008044] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/22/2019] [Indexed: 11/19/2022] Open
Abstract
The development of lateral roots in Arabidopsis thaliana is strongly dependent on signaling directed by the AUXIN RESPONSE FACTOR7 (ARF7), which in turn activates LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16, LBD18 and LBD29). Here, the product of PRH1, a PR-1 homolog annotated previously as encoding a pathogen-responsive protein, was identified as a target of ARF7-mediated auxin signaling and also as participating in the development of lateral roots. PRH1 was shown to be strongly induced by auxin treatment, and plants lacking a functional copy of PRH1 formed fewer lateral roots. The transcription of PRH1 was controlled by the binding of both ARF7 and LBDs to its promoter region. In Arabidopsis thaliana AUXIN RESPONSE FACTOR7 (ARF7)-mediated auxin signaling plays a key role in lateral roots (LRs) development. The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16, LBD18 and LBD29) act downstream of ARF7-mediated auxin signaling to control LRs formation. Here, the PR-1 homolog PRH1 was identified as a novel target of both ARF7 and LBDs (especially the LBD29) during auxin induced LRs formation, as both ARF7 and LBDs were able to bind to the PRH1 promoter. This study provides new insights about how auxin regulates lateral root development.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Wenqing Tao
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Ruiqi Sun
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Junxia Wang
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Cuiling Li
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Xiangpei Kong
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Huiyu Tian
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhaojun Ding
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
- * E-mail:
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Santos Teixeira JA, Ten Tusscher KH. The Systems Biology of Lateral Root Formation: Connecting the Dots. MOLECULAR PLANT 2019; 12:784-803. [PMID: 30953788 DOI: 10.1016/j.molp.2019.03.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/20/2019] [Accepted: 03/26/2019] [Indexed: 05/29/2023]
Abstract
The root system is a major determinant of a plant's access to water and nutrients. The architecture of the root system to a large extent depends on the repeated formation of new lateral roots. In this review, we discuss lateral root development from a systems biology perspective. We focus on studies combining experiments with computational modeling that have advanced our understanding of how the auxin-centered regulatory modules involved in different stages of lateral root development exert their specific functions. Moreover, we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next, a subject that thus far has received limited attention. In addition, we analyze how environmental factors impinge on these modules, and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making. Finally, we provide some suggestions for extending current models of lateral root development to incorporate multiple processes and stages. Only through more comprehensive models we can fully elucidate the cooperative effects of multiple processes on later root formation, and how one stage drives the transition to the next.
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Affiliation(s)
- J A Santos Teixeira
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - K H Ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, the Netherlands.
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7
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Cho C, Jeon E, Pandey SK, Ha SH, Kim J. LBD13 positively regulates lateral root formation in Arabidopsis. PLANTA 2019; 249:1251-1258. [PMID: 30627888 DOI: 10.1007/s00425-018-03087-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/29/2018] [Indexed: 05/26/2023]
Abstract
Lateral Organ Boundaries Domain 13 (LBD13), which is expressed in emerged lateral roots and encodes a transcriptional activator, plays an important role in lateral root formation in Arabidopsis. Lateral roots (LRs) are major determinants of root system architecture, contributing to the survival strategies of plants. Members of the LBD gene family encode plant-specific transcription factors that play key roles in plant organ development. Several LBD genes, such as LBD14, 16, 18, 29, and 33, have been shown to play important roles in regulating LR development in Arabidopsis. In the present study, we show that LBD13 is expressed in emerged LRs and LR meristems of elongated LRs and regulates LR formation in Arabidopsis. Transient gene expression assays with Arabidopsis protoplasts showed that LBD13 is localized to the nucleus and harbors transcription-activating potential. Knock-down of LBD13 expression by RNA interference resulted in reduced LR formation, whereas overexpression of LBD13 enhanced LR formation in transgenic Arabidopsis. Analysis of β-glucuronidase (GUS) expression under the control of the LBD13 promoter showed that GUS staining was detected in LRs emerged from the primary root, but not in LR primordia. Moreover, both the distribution of LR primordium number and developmental kinetics of LR primordia were not affected either by knock-down or by overexpression of LBD13. Taken together, these results suggest that LBD13 is a nuclear-localized transcriptional activator and controls LR formation during or after LR emergence.
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Affiliation(s)
- Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Eunkyeong Jeon
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Shashank K Pandey
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Se Hoon Ha
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea.
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, South Korea.
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Pandey SK, Lee HW, Kim MJ, Cho C, Oh E, Kim J. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:233-251. [PMID: 29681137 DOI: 10.1111/tpj.13945] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/10/2023]
Abstract
A hierarchy of transcriptional regulators controlling lateral root formation in Arabidopsis thaliana has been identified, including the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19-LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16)/LBD18 transcriptional network; however, their feedback regulation mechanisms are not known. Here we show that LBD18 controls ARF activity using the dual mode of a positive feedback loop. We showed that ARF7 and ARF19 directly bind AuxRE in the LBD18 promoter. A variety of molecular and biochemical experiments demonstrated that LBD18 binds a specific DNA motif in the ARF19 promoter to regulate its expression in vivo as well as in vitro. LBD18 interacts with ARFs including ARF7 and ARF19 via the Phox and Bem1 domain of ARF to enhance the transcriptional activity of ARF7 on AuxRE, and competes with auxin/indole-3-acetic acid (IAA) repressors for ARF binding, overriding the negative feedback loop exerted by Aux/IAA repressors. Taken together, these results show that LBD18 and ARFs form a double positive feedback loop, and that LBD18 uses the dual mode of a positive feedback loop by binding directly to the ARF19 promoter and through the protein-protein interactions with ARF7 and ARF19. This novel mechanism of feedback loops may constitute a robust feedback mechanism that ensures continued lateral root growth in response to auxin in Arabidopsis.
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Affiliation(s)
- Shashank K Pandey
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Han Woo Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Min-Jung Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Eunkyoo Oh
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
- Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
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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: 197] [Impact Index Per Article: 32.8] [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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10
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Abstract
In plants, the transcription factor families have been implicated in many important biological processes. These processes include morphogenesis, signal transduction and environmental stress responses. Proteins containing the lateral organ boundaries domain (LBD), which encodes a zinc finger-like domain are only found in plants. This finding indicates that this unique gene family regulates only plant-specific biological processes. LBD genes play crucial roles in the growth and development of plants such as Arabidopsis, Oryza sativa, Zea mays, poplar, apple and tomato. However, relatively little is known about the LBD genes in grape (Vitis vinifera). In this study, we identified 40 LBD genes in the grape genome. A complete overview of the chromosomal locations, phylogenetic relationships, structures and expression profiles of this gene family during development in grape is presented here. Phylogenetic analysis showed that the LBD genes could be divided into classes I and II, together with LBDs from Arabidopsis. We mapped the 40 LBD genes on the grape chromosomes (chr1-chr19) and found that 37 of the predicted grape LBD genes were distributed in different densities across 12 chromosomes. Grape LBDs were found to share a similar intron/exon structure and gene length within the same class. The expression profiles of grape LBD genes at different developmental stages were analysed using microarray data. Results showed that 21 grape LBD genes may be involved in grape developmental processes, including preveraison, veraison and ripening. Finally, we analysed the expression patterns of six LBD genes through quantitative real-time polymerase chain reation analysis. The six LBD genes showed differential expression patterns among the three representative grape tissues, and five of these genes were found to be involved in responses to mannitol, sodium chloride, heat stress and low temperature treatments. To our knowledge, this is the first study to analyse the LBD gene family in grape and provides valuable information for classification and functional investigation of this gene family.
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Kim M, Kim MJ, Pandey S, Kim J. Expression and Protein Interaction Analyses Reveal Combinatorial Interactions of LBD Transcription Factors During Arabidopsis Pollen Development. PLANT & CELL PHYSIOLOGY 2016; 57:2291-2299. [PMID: 27519310 DOI: 10.1093/pcp/pcw145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor gene family members play key roles in diverse aspects of plant development. LBD10 and LBD27 have been shown to be essential for pollen development in Arabidopsis thaliana. From the previous RNA sequencing (RNA-Seq) data set of Arabidopsis pollen, we identified the mRNAs of LBD22, LBD25 and LBD36 in addition to LBD10 and LBD27 in Arabidopsis pollen. Here we conducted expression and cellular analysis using GFP:GUS (green fluorescent protein:β-glucuronidase) reporter gene and subcellular localization assays using LBD:GFP fusion proteins expressed under the control of their own promoters in Arabidopsis. We found that these LBD proteins display spatially and temporally distinct and overlapping expression patterns during pollen development. Bimolecular fluorescence complementation and GST (glutathione S-transferase) pull-down assays demonstrated that protein-protein interactions occur among the LBDs exhibiting overlapping expression during pollen development. We further showed that LBD10, LBD22, LBD25, LBD27 and LBD36 interact with each other to form heterodimers, which are localized to the nucleus in Arabidopsis protoplasts. Taken together, these results suggest that combinatorial interactions among LBD proteins may be important for their function in pollen development in Arabidopsis.
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Affiliation(s)
- Mirim Kim
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Korea
| | - Min-Jung Kim
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Korea
| | - Shashank Pandey
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, Korea
- Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea
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12
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Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benkova E, Fukaki H, Brady SM, Scheres B, Péret B, Bennett MJ. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development 2016; 143:3340-9. [PMID: 27578783 DOI: 10.1242/dev.136283] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022]
Abstract
Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.
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Affiliation(s)
- Silvana Porco
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Antoine Larrieu
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Laboratoire Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Yujuan Du
- Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tatsuaki Goh
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kamal Swarup
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Ranjan Swarup
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Britta Kuempers
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Julien Lavenus
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Institute of Plant Sciences, 21 Altenbergrain, Bern 3006, Switzerland
| | - Ilda Casimiro
- Departamento Anatomia, Biologia Celular Y Zoologia, Facultad de Ciencias, Universidad de Extremadura, Badajoz 06006, Spain
| | - Kristine Hill
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Eva Benkova
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ben Scheres
- Molecular Genetics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Benjamin Péret
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK Centre National de la Recherche Scientifique, Biochimie et Physiologie Moléculaire des Plantes, Montpellier SupAgro, 2 Place Pierre Viala, Montpellier 34060, France
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
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13
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Ba LJ, Kuang JF, Chen JY, Lu WJ. MaJAZ1 Attenuates the MaLBD5-Mediated Transcriptional Activation of Jasmonate Biosynthesis Gene MaAOC2 in Regulating Cold Tolerance of Banana Fruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:738-745. [PMID: 26760434 DOI: 10.1021/acs.jafc.5b05005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Previous studies indicated that methyl jasmonate (MeJA) treatment could effectively reduce the chilling injury of many fruits, including banana, but the underlying mechanism is poorly understood. In this study, one lateral organ boundaries (LOB) domain (LBD) gene, designated as MaLBD5, was isolated and characterized from banana fruit. Expression analysis revealed that accumulation of MaLBD5 was induced by cold temperature and MeJA treatment. Subcellular localization and transactivation assays showed that MaLBD5 was localized to the nucleus and possessed transcriptional activation activity. Protein-protein interaction analysis demonstrated that MaLBD5 physically interacted with MaJAZ1, a potential repressor of jasmonate signaling. Furthermore, transient expression assays indicated that MaLBD5 transactivated a jasmonate biosynthesis gene, termed MaAOC2, which was also induced by cold and MeJA. More interestingly, MaJAZ1 attenuated the MaLBD5-mediated transactivation of MaAOC2. These results suggest that MaLBD5 and MaJAZ1 might act antagonistically in relation to MeJA-induced cold tolerance of banana fruit, at least partially via affecting jasmonate biosynthesis. Collectively, our findings expand the knowledge of the transcriptional regulatory network of MeJA-mediated cold tolerance of banana fruit.
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Affiliation(s)
- Liang-jie Ba
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou, Guangdong 510642, People's Republic of China
| | - Jian-fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou, Guangdong 510642, People's Republic of China
| | - Jian-ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou, Guangdong 510642, People's Republic of China
| | - Wang-jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University , Guangzhou, Guangdong 510642, People's Republic of China
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14
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Xu C, Luo F, Hochholdinger F. LOB Domain Proteins: Beyond Lateral Organ Boundaries. TRENDS IN PLANT SCIENCE 2016; 21:159-167. [PMID: 26616195 DOI: 10.1016/j.tplants.2015.10.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/28/2015] [Accepted: 10/15/2015] [Indexed: 05/07/2023]
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins defined by a conserved LATERAL ORGAN BOUNDARIES (LOB) domain are key regulators of plant organ development. Recent studies have expanded their functional diversity beyond the definition of lateral organ boundaries to pollen development, plant regeneration, photomorphogenesis, pathogen response, and specific developmental functions in non-model plants, such as poplar and legumes. The identification of a range of upstream regulators, protein partners, and downstream targets of LBD family members has unraveled the molecular networks of LBD-dependent processes. Moreover, it has been demonstrated that LBD proteins have essential roles in integrating developmental changes in response to phytohormone signaling or environmental cues. As we discuss here, these novel discoveries of LBD functions and their molecular contexts promote a better understanding of this plant-specific transcription factor family.
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Affiliation(s)
- Changzheng Xu
- Southwest University, College of Environment and Resources, Research Centre of Bioenergy and Bioremediation (RCBB), 400715 Chongqing, China; Southwest University, College of Environment and Resources, Centre of Excellence for Soil Biology (CRE), 400715, Chongqing, China.
| | - Feng Luo
- Southwest University, College of Environment and Resources, Research Centre of Bioenergy and Bioremediation (RCBB), 400715 Chongqing, China
| | - Frank Hochholdinger
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, 53113 Bonn, Germany.
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15
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Cosgrove DJ. Plant expansins: diversity and interactions with plant cell walls. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:162-72. [PMID: 26057089 PMCID: PMC4532548 DOI: 10.1016/j.pbi.2015.05.014] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/11/2015] [Accepted: 05/15/2015] [Indexed: 05/18/2023]
Abstract
Expansins were discovered two decades ago as cell wall proteins that mediate acid-induced growth by catalyzing loosening of plant cell walls without lysis of wall polymers. In the interim our understanding of expansins has gotten more complex through bioinformatic analysis of expansin distribution and evolution, as well as through expression analysis, dissection of the upstream transcription factors regulating expression, and identification of additional classes of expansin by sequence and structural similarities. Molecular analyses of expansins from bacteria have identified residues essential for wall loosening activity and clarified the bifunctional nature of expansin binding to complex cell walls. Transgenic modulation of expansin expression modifies growth and stress physiology of plants, but not always in predictable or even understandable ways.
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Affiliation(s)
- Daniel J Cosgrove
- Department of Biology, Penn State University, University Park, PA 16802, USA.
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16
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Shaikhali J. GIP1 protein is a novel cofactor that regulates DNA-binding affinity of redox-regulated members of bZIP transcription factors involved in the early stages of Arabidopsis development. PROTOPLASMA 2015; 252:867-883. [PMID: 25387999 DOI: 10.1007/s00709-014-0726-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
In response to environmental light signals, gene expression adjustments play an important role in regulation of photomorphogenesis. LHCB2.4 is among the genes responsive to light signals, and its expression is regulated by redox-regulated members of G-group bZIP transcription factors. The biochemical interrelations of GBF1-interacting protein 1 (GIP1) and the G-group bZIP transcription factors have been investigated. GIP1, previously shown to enhance DNA-binding activities of maize GBF1 and Arabidopsis GBF3, is a plant specific protein that reduces DNA-binding activity of AtbZIP16, AtbZIP68, and AtGBF1 under non-reducing conditions through direct physical interaction shown by the yeast two-hybrid and pull-down assays. Fluorescence microscopy studies using cyan fluorescent protein (CFP)-fusion protein indicate that GIP1 is exclusively localized in the nucleus. Under non- reducing conditions, GIP1 exhibits predominantly high molecular weight forms, whereas it predominates in low molecular weight monomers under reducing conditions. While reduced GIP1 induced formation of DNA-protein complexes of G-group bZIPs, oxidized GIP1 decreased the amount of those complexes and instead induced its chaperone function suggesting functional switching from redox to chaperone activity. Finally analysis of transgenic plants overexpressing GIP1 revealed that GIP1 is a negative co-regulator in red and blue light mediated hypocotyl elongation. By regulating the repression effect by bZIP16 and the activation effect by bZIP68 and GBF1 on LHCB2.4 expression, GIP1 functions to promote hypocotyl elongation during the early stages of Arabidopsis seedling development.
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Affiliation(s)
- Jehad Shaikhali
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences SLU, 901 83, Umeå, Sweden,
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