1
|
Shaar-Moshe L, Brady SM. SHORT-ROOT and SCARECROW homologs regulate patterning of diverse cell types within and between species. THE NEW PHYTOLOGIST 2023; 237:1542-1549. [PMID: 36457304 DOI: 10.1111/nph.18654] [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: 08/08/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The roles of SHORT-ROOT (SHR) and SCARECROW (SCR) in ground tissue patterning and differentiation have been well established in the root of Arabidopsis thaliana. Recently, work in additional organs and species revealed the extensive functional diversification of these genes, including regulation of cortical divisions essential for nodule organogenesis in legume roots, bundle sheath specification in the Arabidopsis leaf, patterning of inner leaf cell layers in maize, and stomatal development in rice. The co-option of distinct functions and cell types is attributed to different mechanisms, including paralog retention, spatiotemporal changes in gene expression, and novel protein functions. Elaborating our knowledge of the SHR-SCR module further unravels the developmental regulation that controls diverse forms and functions within and between species.
Collapse
Affiliation(s)
- Lidor Shaar-Moshe
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
| |
Collapse
|
2
|
Jaiswal V, Kakkar M, Kumari P, Zinta G, Gahlaut V, Kumar S. Multifaceted Roles of GRAS Transcription Factors in Growth and Stress Responses in Plants. iScience 2022; 25:105026. [PMID: 36117995 PMCID: PMC9474926 DOI: 10.1016/j.isci.2022.105026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mrinalini Kakkar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Priya Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Corresponding author
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
- Corresponding author
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| |
Collapse
|
3
|
Lou H, Tucker MR, Shirley NJ, Lahnstein J, Yang X, Ma C, Schwerdt J, Fusi R, Burton RA, Band LR, Bennett MJ, Bulone V. The cellulose synthase-like F3 (CslF3) gene mediates cell wall polysaccharide synthesis and affects root growth and differentiation in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1681-1699. [PMID: 35395116 PMCID: PMC9324092 DOI: 10.1111/tpj.15764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The barley cellulose synthase-like F (CslF) genes encode putative cell wall polysaccharide synthases. They are related to the cellulose synthase (CesA) genes involved in cellulose biosynthesis, and the CslD genes that influence root hair development. Although CslD genes are implicated in callose, mannan and cellulose biosynthesis, and are found in both monocots and eudicots, CslF genes are specific to the Poaceae. Recently the barley CslF3 (HvCslF3) gene was shown to be involved in the synthesis of a novel (1,4)-β-linked glucoxylan, but it remains unclear whether this gene contributes to plant growth and development. Here, expression profiling using qRT-PCR and mRNA in situ hybridization revealed that HvCslF3 accumulates in the root elongation zone. Silencing HvCslF3 by RNAi was accompanied by slower root growth, linked with a shorter elongation zone and a significant reduction in root system size. Polymer profiling of the RNAi lines revealed a significant reduction in (1,4)-β-linked glucoxylan levels. Remarkably, the heterologous expression of HvCslF3 in wild-type (Col-0) and root hair-deficient Arabidopsis mutants (csld3 and csld5) complemented the csld5 mutant phenotype, in addition to altering epidermal cell fate. Our results reveal a key role for HvCslF3 during barley root development and suggest that members of the CslD and CslF gene families have similar functions during root growth regulation.
Collapse
Affiliation(s)
- Haoyu Lou
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- Division of Plant and Crop Sciences, School of BioscienceUniversity of NottinghamSutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Matthew R. Tucker
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Neil J. Shirley
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Jelle Lahnstein
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- Adelaide Glycomics, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Xiujuan Yang
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Chao Ma
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Julian Schwerdt
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- Adelaide Glycomics, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Riccardo Fusi
- Division of Plant and Crop Sciences, School of BioscienceUniversity of NottinghamSutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Rachel A. Burton
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
| | - Leah R. Band
- Division of Plant and Crop Sciences, School of BioscienceUniversity of NottinghamSutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
- School of Mathematical SciencesUniversity of NottinghamNottinghamNG7 2RDUK
| | - Malcolm J. Bennett
- Division of Plant and Crop Sciences, School of BioscienceUniversity of NottinghamSutton Bonington Campus, LoughboroughLeicestershireLE12 5RDUK
| | - Vincent Bulone
- School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- Adelaide Glycomics, School of Agriculture, Food and WineUniversity of AdelaideWaite CampusUrrbraeSouth Australia5064Australia
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and HealthRoyal Institute of Technology (KTH), AlbaNova University CentreStockholmSweden
| |
Collapse
|
4
|
Ortiz-Ramírez C, Guillotin B, Xu X, Rahni R, Zhang S, Yan Z, Coqueiro Dias Araujo P, Demesa-Arevalo E, Lee L, Van Eck J, Gingeras TR, Jackson D, Gallagher KL, Birnbaum KD. Ground tissue circuitry regulates organ complexity in maize and Setaria. Science 2021; 374:1247-1252. [PMID: 34855479 DOI: 10.1126/science.abj2327] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Carlos Ortiz-Ramírez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.,UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato 36821, México
| | - Bruno Guillotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ramin Rahni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sanqiang Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Zhe Yan
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 1904, USA
| | | | | | - Laura Lee
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kimberly L Gallagher
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 1904, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| |
Collapse
|
5
|
Chen J, Yan Q, Li J, Feng L, Zhang Y, Xu J, Xia R, Zeng Z, Liu Y. The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn). BMC PLANT BIOLOGY 2021; 21:423. [PMID: 34535087 PMCID: PMC8447652 DOI: 10.1186/s12870-021-03193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The GRAS gene family plays crucial roles in multiple biological processes of plant growth, including seed development, which is related to seedless traits of litchi (Litchi chinensis Sonn.). However, it hasn't been fully identified and analyzed in litchi, an economic fruit tree cultivated in subtropical regions. RESULTS In this study, 48 LcGRAS proteins were identified and termed according to their chromosomal location. LcGRAS proteins can be categorized into 14 subfamilies through phylogenetic analysis. Gene structure and conserved domain analysis revealed that different subfamilies harbored various motif patterns, suggesting their functional diversity. Synteny analysis revealed that the expansion of the GRAS family in litchi may be driven by their tandem and segmental duplication. After comprehensively analysing degradome data, we found that four LcGRAS genes belong to HAM subfamily were regulated via miR171-mediated degradation. The various expression patterns of LcGRAS genes in different tissues uncovered they were involved in different biological processes. Moreover, the different temporal expression profiles of LcGRAS genes between abortive and bold seed indicated some of them were involved in maintaining the normal development of the seed. CONCLUSION Our study provides comprehensive analyses on GRAS family members in litchi, insight into a better understanding of the roles of GRAS in litchi development, and lays the foundation for further investigations on litchi seed development.
Collapse
Affiliation(s)
- Jingwen Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qian Yan
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture / Guangdong ProvinceKey Laboratary of Tropical and Subtropical Fruit Tree Research / Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jiawei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Lei Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
| |
Collapse
|
6
|
Cui H. Challenges and Approaches to Crop Improvement Through C3-to-C4 Engineering. FRONTIERS IN PLANT SCIENCE 2021; 12:715391. [PMID: 34594351 PMCID: PMC8476962 DOI: 10.3389/fpls.2021.715391] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/06/2021] [Indexed: 05/24/2023]
Abstract
With a rapidly growing world population and dwindling natural resources, we are now facing the enormous challenge of increasing crop yields while simultaneously improving the efficiency of resource utilization. Introduction of C4 photosynthesis into C3 crops is widely accepted as a key strategy to meet this challenge because C4 plants are more efficient than C3 plants in photosynthesis and resource usage, particularly in hot climates, where the potential for productivity is high. Lending support to the feasibility of this C3-to-C4 engineering, evidence indicates that C4 photosynthesis has evolved from C3 photosynthesis in multiple lineages. Nevertheless, C3-to-C4 engineering is not an easy task, as several features essential to C4 photosynthesis must be introduced into C3 plants. One such feature is the spatial separation of the two phases of photosynthesis (CO2 fixation and carbohydrate synthesis) into the mesophyll and bundle sheath cells, respectively. Another feature is the Kranz anatomy, characterized by a close association between the mesophyll and bundle sheath (BS) cells (1:1 ratio). These anatomical features, along with a C4-specific carbon fixation enzyme (PEPC), form a CO2-concentration mechanism that ensures a high photosynthetic efficiency. Much effort has been taken in the past to introduce the C4 mechanism into C3 plants, but none of these attempts has met with success, which is in my opinion due to a lack of system-level understanding and manipulation of the C3 and C4 pathways. As a prerequisite for the C3-to-C4 engineering, I propose that not only the mechanisms that control the Kranz anatomy and cell-type-specific expression in C3 and C4 plants must be elucidated, but also a good understanding of the gene regulatory network underlying C3 and C4 photosynthesis must be achieved. In this review, I first describe the past and current efforts to increase photosynthetic efficiency in C3 plants and their limitations; I then discuss a systems approach to tackling down this challenge, some practical issues, and recent technical innovations that would help us to solve these problems.
Collapse
Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- College of Life Science, Northwest Science University of Agriculture and Forestry, Yangling, China
| |
Collapse
|
7
|
Ruiz-Aguilar B, Raya-González J, López-Bucio JS, Reyes de la Cruz H, Herrera-Estrella L, Ruiz-Herrera LF, Martínez-Trujillo M, López-Bucio J. Mutation of MEDIATOR 18 and chromate trigger twinning of the primary root meristem in Arabidopsis. PLANT, CELL & ENVIRONMENT 2020; 43:1989-1999. [PMID: 32400913 DOI: 10.1111/pce.13786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/25/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Plants adapt to soil injury and biotic stress via cell regeneration. In Arabidopsis, root tip damage by genotoxic agents, antibiotics, UV light and cutting induces a program that recovers the missing tissues through activation of stem cells and involves ethylene response factor 115 (ERF115), which triggers cell replenishment. Here, we show that mutation of the gene encoding an MED18 subunit of the transcriptional MEDIATOR complex and chromate [Cr(VI)], an environmental pollutant, synergistically trigger a developmental program that enables the splitting of the meristem in vivo to produce twin roots. Expression of the quiescent centre gene marker WOX5, auxin-inducible DR5:GFP reporter and the ERF115 factor traced the changes in cell identity during the conversion of single primary root meristems into twin roots and were induced in an MED18 and chromate-dependent manner during the root twinning events, which also required auxin redistribution and signalling mediated by IAA14/SOLITARY ROOT (SLR1). Splitting of the root meristem allowed dichotomous root branching in Arabidopsis, a poorly understood process in which stem cells may act to enable whole organ regeneration.
Collapse
Affiliation(s)
- Bricia Ruiz-Aguilar
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Javier Raya-González
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Jesús Salvador López-Bucio
- CONACYT, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio B3, Ciudad Universitaria, Morelia, Mexico
| | - Homero Reyes de la Cruz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Luis Herrera-Estrella
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Campus Irapuato, Guanajuato, Mexico
| | - León Francisco Ruiz-Herrera
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Miguel Martínez-Trujillo
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo. Edificio R, Ciudad Universitaria, Morelia, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| |
Collapse
|
8
|
Niu X, Chen S, Li J, Liu Y, Ji W, Li H. Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1. BMC Genomics 2019; 20:635. [PMID: 31387534 PMCID: PMC6683515 DOI: 10.1186/s12864-019-5985-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically analyzed in Brachypodium distachyon, a new model grass. Results In this study, 48 BdGRAS genes were identified. Duplicated genes account for 41.7% of them and contribute to the expansion of this gene family. 33, 39, 35 and 35 BdGRAS genes were identified by synteny with their orthologs in rice, sorghum, maize and wheat genome, respectively, indicating close relationships among these species. Based on their phylogenic relationships to GRAS genes in rice and maize, BdGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar protein sequences, conserved motifs and gene structures, suggesting possible conserved functions. Although expression variation is high, some BdGRAS genes are tissue-specific, phytohormones- or abiotic stresses-responsive, and they may play key roles in development, signal transduction pathways and stress responses. In addition, DELLA genes BdSLR1 and BdSLRL1 were functionally characterized to play a role in plant growth via the GA signal pathway, consistent with GO annotations and KEGG pathway analyses. Conclusions Systematic analyses of BdGRAS genes indicated that members of the same subfamily may play similar roles. This was supported by the conserved functions of BdSLR1 and BdSLRL1 in GA pathway. These results laid a foundation for further functional elucidation of BdGRAS genes, especially, BdSLR1 and BdSLRL1. Electronic supplementary material The online version of this article (10.1186/s12864-019-5985-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Jiawei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
9
|
Efroni I. A Conceptual Framework for Cell Identity Transitions in Plants. PLANT & CELL PHYSIOLOGY 2018; 59:691-701. [PMID: 29136202 PMCID: PMC6018971 DOI: 10.1093/pcp/pcx172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/27/2017] [Indexed: 05/19/2023]
Abstract
Multicellular organisms develop from a single cell that proliferates to form different cell types with specialized functions. Sixty years ago, Waddington suggested the 'epigenetic landscape' as a useful metaphor for the process. According to this view, cells move through a rugged identity space along genetically encoded trajectories, until arriving at one of the possible final fates. In plants in particular, these trajectories have strong spatial correlates, as cell identity is intimately linked to its relative position within the plant. During regeneration, however, positional signals are severely disrupted and differentiated cells are able to undergo rapid non-canonical identity changes. Moreover, while pluripotent properties have long been ascribed to plant cells, the introduction of induced pluripotent stem cells in animal studies suggests such plasticity may not be unique to plants. As a result, current concepts of differentiation as a gradual and hierarchical process are being reformulated across biological fields. Traditional studies of plant regeneration have placed strong emphasis on the emergence of patterns and tissue organization, and information regarding the events occurring at the level of individual cells is only now beginning to emerge. Here, I review the historical and current concepts of cell identity and identity transitions, and discuss how new views and tools may instruct the future understanding of differentiation and plant regeneration.
Collapse
Affiliation(s)
- Idan Efroni
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot, Israel
| |
Collapse
|
10
|
Li P, Yang M, Chang J, Wu J, Zhong F, Rahman A, Qin H, Wu S. Spatial Expression and Functional Analysis of Casparian Strip Regulatory Genes in Endodermis Reveals the Conserved Mechanism in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:832. [PMID: 29988388 PMCID: PMC6024017 DOI: 10.3389/fpls.2018.00832] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/29/2018] [Indexed: 05/20/2023]
Abstract
Casparian strip (CS) is an impregnation of endodermal cell wall, forming an apoplastic diffusion barrier which forces the symplastic and selective transport of nutrients across endodermis. This extracellular structure can be found in the roots of all higher plants and is thought to provide the protection of vascular tissues. In Arabidopsis, a genetic toolbox regulating the formation of Casparian strips has emerged recently. However, Arabidopsis has the stereotypical root which is much simpler than most other plant species. To understand the Casparian strip formation in a more complex root system, we examined CS regulatory pathways in tomato. Our results reveal a spatiotemporally conserved expression pattern of most essential components of CS machinery in tomato. Further functional analyses verify the role of homologous CS genes in the Casparian strip formation in tomato, indicating the functional conservation of CS regulatory cascade in tomato.
Collapse
Affiliation(s)
- Pengxue Li
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meina Yang
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiang Chang
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junqing Wu
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fenglin Zhong
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Abidur Rahman
- Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Haiyang Qin
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuang Wu
- FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Shuang Wu,
| |
Collapse
|
11
|
Identification and expression of GRAS family genes in maize (Zea mays L.). PLoS One 2017; 12:e0185418. [PMID: 28957440 PMCID: PMC5619761 DOI: 10.1371/journal.pone.0185418] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 09/12/2017] [Indexed: 02/01/2023] Open
Abstract
GRAS transcriptional factors have diverse functions in plant growth and development, and are named after the first three transcription factors, namely, GAI (GIBBERELLIC ACID INSENSITIVE), RGA (REPRESSOR OF GAI) and SCR (SCARECROW) identified in this family. Knowledge of the GRAS gene family in maize remains was largely unknown, and their characterization is necessary to understand their importance in the maize life cycle. This study identified 86 GRAS genes in maize, and further characterized with phylogenetics, gene structural analysis, genomic loci, and expression patterns. The 86 GRAS genes were divided into 8 groups (SCL3, HAM, LS, SCR, DELLA, SHR, PAT1 and LISCL) by phylogenetic analysis. Most of the maize GRAS genes contain one exon (80.23%) and closely related members in the phylogenetic tree had similar structure and motif composition. Different motifs especially in the N-terminus might be the sources of their functional divergence. Segmental- and tandem-duplication occurred in this family leading to expansion of maize GRAS genes and the expression patterns of the duplicated genes in the heat map according to the published microarray data were very similar. Quantitative RT-PCR (qRT-PCR) results demonstrated that the expression level of genes in different tissues were different, suggesting their differential roles in plant growth and development. The data set expands our knowledge to understanding the function of GRAS genes in maize, an important crop plant in the world.
Collapse
|
12
|
Bai Z, Xia P, Wang R, Jiao J, Ru M, Liu J, Liang Z. Molecular cloning and characterization of five SmGRAS genes associated with tanshinone biosynthesis in Salvia miltiorrhiza hairy roots. PLoS One 2017; 12:e0185322. [PMID: 28953930 PMCID: PMC5617194 DOI: 10.1371/journal.pone.0185322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/11/2017] [Indexed: 01/31/2023] Open
Abstract
The gibberellin-responsive element binding factor (GRAS) family of proteins plays an important role in the transcriptional regulation of plant development and hormone signaling. To date, there are no reports on GRAS family proteins expressed in Salvia miltiorrhiza. In this study, 28 ESTs that contained the GRAS domain were identified from a S. miltiorrhiza cDNA library. Of these, full-length sequences of five genes were cloned and sequence analysis indicated that all five proteins contain only one GRAS domain and therefore, belong to the GRAS family. The five genes were designated S. miltiorrhiza GRAS1-5 (SmGRAS1-5), which belong to groups I (SmGRAS2 and SmGRAS4), II (SmGRAS3), III (SmGRAS1), and VIII (SmGRAS5) respectively. Additionally, SmGRAS1-5 have different expression patterns in the reed head, stems, leaves, flowers, and roots of S. miltiorrhiza. In this study, the expression of SmGRAS1-5 was sensitive to Gibberellin (GA) stress and that of SmGRAS1, SmGRAS4 and SmGRAS5 was sensitive to Ethephon (Eth) stress respectively. Moreover, S. miltiorrhiza copalyl diphosphate synthases 1 (SmCPS1) and S. miltiorrhiza kaurene synthase like 1 (SmKSL1), which are two key enzymes gene in the diterpenoid biosynthesis pathway, were also response to GA and Eth stress. In addition, Dihydrotanshinone (DT-I) and Tanshinone I (T-I) content were enhanced by GA and Eth stress, Tanshinone IIA (T-IIA) content was increased by GA stress, and the accumulation of Cryptotanshinone (CT) was insensitive to both GA and Eth stress. Together, these results provide insights into functional conservation and diversification of SmGRASs and are useful information for further elucidating SmGRAS functions.
Collapse
Affiliation(s)
- Zhenqing Bai
- College of Life Science, Northwest A&F University, Yangling, China
| | - Pengguo Xia
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ruilin Wang
- College of Life Science, Northwest A&F University, Yangling, China
| | - Jie Jiao
- College of Life Science, Northwest A&F University, Yangling, China
| | - Mei Ru
- College of Life Science, Northwest A&F University, Yangling, China
| | - Jingling Liu
- College of Life Science, Northwest A&F University, Yangling, China
| | - Zongsuo Liang
- College of Life Science, Northwest A&F University, Yangling, China
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
- * E-mail:
| |
Collapse
|
13
|
Kirschner GK, Stahl Y, Von Korff M, Simon R. Unique and Conserved Features of the Barley Root Meristem. FRONTIERS IN PLANT SCIENCE 2017; 8:1240. [PMID: 28785269 PMCID: PMC5519606 DOI: 10.3389/fpls.2017.01240] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/30/2017] [Indexed: 05/20/2023]
Abstract
Plant root growth is enabled by root meristems that harbor the stem cell niches as a source of progenitors for the different root tissues. Understanding the root development of diverse plant species is important to be able to control root growth in order to gain better performances of crop plants. In this study, we analyzed the root meristem of the fourth most abundant crop plant, barley (Hordeum vulgare). Cell division studies revealed that the barley stem cell niche comprises a Quiescent Center (QC) of around 30 cells with low mitotic activity. The surrounding stem cells contribute to root growth through the production of new cells that are displaced from the meristem, elongate and differentiate into specialized root tissues. The distal stem cells produce the root cap and lateral root cap cells, while cells lateral to the QC generate the epidermis, as it is typical for monocots. Endodermis and inner cortex are derived from one common initial lateral to the QC, while the outer cortex cell layers are derived from a distinct stem cell. In rice and Arabidopsis, meristem homeostasis is achieved through feedback signaling from differentiated cells involving peptides of the CLE family. Application of synthetic CLE40 orthologous peptide from barley promotes meristem cell differentiation, similar to rice and Arabidopsis. However, in contrast to Arabidopsis, the columella stem cells do not respond to the CLE40 peptide, indicating that distinct mechanisms control columella cell fate in monocot and dicot plants.
Collapse
Affiliation(s)
- Gwendolyn K. Kirschner
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorf, Germany
- Institute for Plant Genetics, Heinrich Heine UniversityDüsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine UniversityDüsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorf, Germany
| | - Maria Von Korff
- Institute for Plant Genetics, Heinrich Heine UniversityDüsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine UniversityDüsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine UniversityDüsseldorf, Germany
| |
Collapse
|
14
|
Wang Z, Yin Y, Hua J, Fan W, Yu C, Xuan L, Yu F. Cloning and Characterization of ThSHRs and ThSCR Transcription Factors in Taxodium Hybrid 'Zhongshanshan 406'. Genes (Basel) 2017; 8:genes8070185. [PMID: 28726763 PMCID: PMC5541318 DOI: 10.3390/genes8070185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/03/2017] [Accepted: 07/17/2017] [Indexed: 01/25/2023] Open
Abstract
Among the GRAS family of transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR) are key regulators of the formation of root tissues. In this study, we isolated and characterized two genes encoding SHR proteins and one gene encoding an SCR protein: ThSHR1 (Accession Number MF045148), ThSHR2 (Accession Number MF045149) and ThSCR (Accession Number MF045152) in the adventitious roots of Taxodium hybrid ‘Zhongshanshan’. Gene structure analysis indicated that ThSHR1, ThSHR2 and ThSCR are all intron free. Multiple protein sequence alignments showed that each of the corresponding proteins, ThSHR1, ThSHR2 and ThSCR, contained five well-conserved domains: leucine heptad repeat I (LHRI), the VHIID motif, leucine heptad repeat II (LHR II), the PFYRE motif, and the SAW motif. The phylogenetic analysis indicated that ThSCR was positioned in the SCR clade with the SCR proteins from eight other species, while ThSHR1 and ThSHR2 were positioned in the SHR clade with the SHR proteins from six other species. Temporal expression patterns of these genes were profiled during the process of adventitious root development on stem cuttings. Whereas expression of both ThSHR2 and ThSCR increased up to primary root formation before declining, that of ThSHR1 increased steadily throughout adventitious root formation. Subcellular localization studies in transgenic poplar protoplasts revealed that ThSHR1, ThSHR2 and ThSCR were localized in the nucleus. Collectively, these results suggest that the three genes encode Taxodium GRAS family transcription factors, and the findings contribute to improving our understanding of the expression and function of SHR and SCR during adventitious root production, which may then be manipulated to achieve high rates of asexual propagation of valuable tree species.
Collapse
Affiliation(s)
- Zhiquan Wang
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China.
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Yunlong Yin
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China.
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Wencai Fan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Lei Xuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Fangyuan Yu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
15
|
Liu H, Qin J, Fan H, Cheng J, Li L, Liu Z. Genome-wide identification, phylogeny and expression analyses of SCARECROW- LIKE( SCL) genes in millet ( Setaria italica). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:629-640. [PMID: 28878501 PMCID: PMC5567716 DOI: 10.1007/s12298-017-0455-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/13/2017] [Accepted: 05/29/2017] [Indexed: 06/04/2023]
Abstract
As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis, maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis-elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C4 photosynthesis and bioenergy studies.
Collapse
Affiliation(s)
- Hongyun Liu
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Jiajia Qin
- School of Physical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Hui Fan
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Jinjin Cheng
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Lin Li
- College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Zheng Liu
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| |
Collapse
|
16
|
Tai H, Opitz N, Lithio A, Lu X, Nettleton D, Hochholdinger F. Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:403-414. [PMID: 28204533 PMCID: PMC5444478 DOI: 10.1093/jxb/erw422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Seminal roots of maize are pivotal for early seedling establishment. The maize mutant rootless concerning crown and seminal roots (rtcs) is defective in seminal root initiation during embryogenesis. In this study, the transcriptomes of wild-type and rtcs embryos were analyzed by RNA-Seq based on histological results at three stages of seminal root primordia formation. Hierarchical clustering highlighted that samples of each genotype grouped together along development. Determination of their gene activity status revealed hundreds of genes specifically transcribed in wild-type or rtcs embryos, while K-mean clustering revealed changes in gene expression dynamics between wild-type and rtcs during embryo development. Pairwise comparisons of rtcs and wild-type embryo transcriptomes identified 131 transcription factors among 3526 differentially expressed genes [false discovery rate (FDR) <5% and |log2Fc|≥1]. Among those, functional annotation highlighted genes involved in cell cycle control and phytohormone action, particularly auxin signaling. Moreover, in silico promoter analyses identified putative RTCS target genes associated with transcription factor action and hormone metabolism and signaling. Significantly, non-syntenic genes that emerged after the separation of maize and sorghum were over-represented among genes displaying RTCS-dependent expression during seminal root primordia formation. This might suggest that these non-syntenic genes came under the transcriptional control of the syntenic gene rtcs during seminal root evolution. Taken together, this study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation.
Collapse
Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Bonn, Germany
| |
Collapse
|
17
|
Yu P, Eggert K, von Wirén N, Li C, Hochholdinger F. Cell Type-Specific Gene Expression Analyses by RNA Sequencing Reveal Local High Nitrate-Triggered Lateral Root Initiation in Shoot-Borne Roots of Maize by Modulating Auxin-Related Cell Cycle Regulation. PLANT PHYSIOLOGY 2015; 169:690-704. [PMID: 26198256 PMCID: PMC4577424 DOI: 10.1104/pp.15.00888] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 05/18/2023]
Abstract
Plants have evolved a unique plasticity of their root system architecture to flexibly exploit heterogeneously distributed mineral elements from soil. Local high concentrations of nitrate trigger lateral root initiation in adult shoot-borne roots of maize (Zea mays) by increasing the frequency of early divisions of phloem pole pericycle cells. Gene expression profiling revealed that, within 12 h of local high nitrate induction, cell cycle activators (cyclin-dependent kinases and cyclin B) were up-regulated, whereas repressors (Kip-related proteins) were down-regulated in the pericycle of shoot-borne roots. In parallel, a ubiquitin protein ligase S-Phase Kinase-Associated Protein1-cullin-F-box protein(S-Phase Kinase-Associated Protein 2B)-related proteasome pathway participated in cell cycle control. The division of pericycle cells was preceded by increased levels of free indole-3-acetic acid in the stele, resulting in DR5-red fluorescent protein-marked auxin response maxima at the phloem poles. Moreover, laser-capture microdissection-based gene expression analyses indicated that, at the same time, a significant local high nitrate induction of the monocot-specific PIN-FORMED9 gene in phloem pole cells modulated auxin efflux to pericycle cells. Time-dependent gene expression analysis further indicated that local high nitrate availability resulted in PIN-FORMED9-mediated auxin efflux and subsequent cell cycle activation, which culminated in the initiation of lateral root primordia. This study provides unique insights into how adult maize roots translate information on heterogeneous nutrient availability into targeted root developmental responses.
Collapse
Affiliation(s)
- Peng Yu
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Kai Eggert
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Nicolaus von Wirén
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Chunjian Li
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Frank Hochholdinger
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| |
Collapse
|
18
|
Huang W, Xian Z, Kang X, Tang N, Li Z. Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC PLANT BIOLOGY 2015; 15:209. [PMID: 26302743 PMCID: PMC4549011 DOI: 10.1186/s12870-015-0590-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/11/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits. RESULTS In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated. CONCLUSIONS This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.
Collapse
Affiliation(s)
- Wei Huang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhiqiang Xian
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Xia Kang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Ning Tang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| |
Collapse
|
19
|
Cui H, Kong D, Liu X, Hao Y. SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:319-27. [PMID: 24517883 DOI: 10.1111/tpj.12470] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/30/2014] [Accepted: 02/03/2014] [Indexed: 05/25/2023]
Abstract
Bundle sheath (BS) cells form a single cell layer surrounding the vascular tissue in leaves. In C3 plants, photosynthesis occurs in both the BS and mesophyll cells, but the BS cells are the major sites of photosynthesis in C4 plants, whereas the mesophyll cells are only involved in CO2 fixation. Because C4 plants are more efficient photosynthetically, introduction of the C4 mechanism into C3 plants is considered a key strategy to improve crop yield. One prerequisite for such C3-to-C4 engineering is the ability to manipulate the number and physiology of the BS cells, but the molecular basis of BS cell-fate specification remains unclear. Here we report that mutations in three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCARECROW-LIKE 23 (SCL23), affect BS cell fate in Arabidopsis thaliana. SCR and SCL23 are expressed specifically in the BS cells and act redundantly in BS cell-fate specification, but their expression pattern and function diverge at later stages of leaf development. Using ChIP-chip experiments and sugar assays, we show that SCR is primarily involved in sugar transport whereas SCL23 functions in mineral transport. SHR is also essential for BS cell-fate specification, but it is expressed in the central vascular tissue. However, the SHR protein moves into the BS cells, where it directly regulates SCR and SCL23 expression. SHR, SCR and SCL23 homologs are present in many plant species, suggesting that this developmental pathway for BS cell-fate specification is likely to be evolutionarily conserved.
Collapse
Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
| | | | | | | |
Collapse
|
20
|
Gao X, Wang C, Cui H. Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. PLANT SIGNALING & BEHAVIOR 2014; 9:29162. [PMID: 24819776 PMCID: PMC4203720 DOI: 10.4161/psb.29162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/08/2014] [Indexed: 05/31/2023]
Abstract
Spatial compartmentation of the photosynthetic process between bundle sheath (BS) cells and mesophyll cells is one of the features that increase the productivity of C4 plants. To introduce C photosynthesis into C3 plants therefore calls for the identification of factors that control BS cell fate and promoter sequences that confer gene expression specifically in the BS and mesophyll cells. We recently demonstrated that three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCR-LIKE 23 (SCL 23), are required for BS cell fate specification in Arabidopsis thaliana. Homologs to these genes are present in other plant species, C3 and C4, suggesting a conserved mechanism for BS cell fate specification. Interestingly, initially SCR and SCL23 are expressed uniformly in BS cells, but at later stages of leaf development SCR expression becomes restricted to the BS cells associated with the phloem, whereas SCL23 is preferentially expressed in the BS cells abutting the xylem. Characterization of the functions and expression patterns of SHR, SCR and SCL23 homologs in other plants, especially C3 crops, will not only advance the knowledge about BS cell development but also provide new tools for manipulating the number and physiology of BS cells, a critical prerequisite for C3-to-C4 engineering.
Collapse
Affiliation(s)
- Xiaorong Gao
- Department of Biological Science; Florida State University; Tallahassee, FL USA
- School of Life Science & Biotechnology; Dalian University of Technology; No. 2 Linggong Road; Dalian PR China
| | - Chaolun Wang
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Hongchang Cui
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| |
Collapse
|
21
|
Hong LW, Yan DW, Liu WC, Chen HG, Lu YT. TIME FOR COFFEE controls root meristem size by changes in auxin accumulation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:275-86. [PMID: 24277277 PMCID: PMC3883298 DOI: 10.1093/jxb/ert374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Roots play important roles in plant survival and productivity as they not only anchor the plants in the soil but are also the primary organ for the uptake of nutrients from the outside. The growth and development of roots depend on the specification and maintenance of the root meristem. Here, we report a previously unknown role of TIME FOR COFFEE (TIC) in controlling root meristem size in Arabidopsis. The results showed that loss of function of TIC reduced root meristem length and cell number by decreasing the competence of meristematic cells to divide. This was due to the repressed expression of PIN genes for decreased acropetal auxin transport in tic-2, leading to low auxin accumulation in the roots responsible for reduced root meristem, which was verified by exogenous application of indole-3-acetic acid. Downregulated expression of PLETHORA1 (PLT1) and PLT2, key transcription factors in mediating the patterning of the root stem cell niche, was also assayed in tic-2. Similar results were obtained with tic-2 and wild-type plants at either dawn or dusk. We also suggested that the MYC2-mediated jasmonic acid signalling pathway may not be involved in the regulation of TIC in controlling the root meristem. Taken together, these results suggest that TIC functions in an auxin-PLTs loop for maintenance of post-embryonic root meristem.
Collapse
Affiliation(s)
- Li-Wei Hong
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Da-Wei Yan
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Wen-Cheng Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Hong-Guo Chen
- College of Chemistry and Biology, Hubei University of Science and Technology, Xianning 437100, Hubei Province, PR China
| | - Ying-Tang Lu
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
22
|
Gao X, Wang C, Cui H. Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. PLANT SIGNALING & BEHAVIOR 2014; 9:e29162. [PMID: 24819776 PMCID: PMC4203720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/08/2014] [Indexed: 02/28/2024]
Abstract
Spatial compartmentation of the photosynthetic process between bundle sheath (BS) cells and mesophyll cells is one of the features that increase the productivity of C4 plants. To introduce C photosynthesis into C3 plants therefore calls for the identification of factors that control BS cell fate and promoter sequences that confer gene expression specifically in the BS and mesophyll cells. We recently demonstrated that three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCR-LIKE 23 (SCL 23), are required for BS cell fate specification in Arabidopsis thaliana. Homologs to these genes are present in other plant species, C3 and C4, suggesting a conserved mechanism for BS cell fate specification. Interestingly, initially SCR and SCL23 are expressed uniformly in BS cells, but at later stages of leaf development SCR expression becomes restricted to the BS cells associated with the phloem, whereas SCL23 is preferentially expressed in the BS cells abutting the xylem. Characterization of the functions and expression patterns of SHR, SCR and SCL23 homologs in other plants, especially C3 crops, will not only advance the knowledge about BS cell development but also provide new tools for manipulating the number and physiology of BS cells, a critical prerequisite for C3-to-C4 engineering.
Collapse
Affiliation(s)
- Xiaorong Gao
- Department of Biological Science; Florida State University; Tallahassee, FL USA
- School of Life Science & Biotechnology; Dalian University of Technology; No. 2 Linggong Road; Dalian PR China
| | - Chaolun Wang
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Hongchang Cui
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| |
Collapse
|
23
|
Slewinski TL, Anderson AA, Zhang C, Turgeon R. Scarecrow plays a role in establishing Kranz anatomy in maize leaves. PLANT & CELL PHYSIOLOGY 2012; 53:2030-7. [PMID: 23128603 DOI: 10.1093/pcp/pcs147] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
More than a quarter of the primary productivity on land, and a large fraction of the food that humans consume, is contributed by plants that fix atmospheric CO(2) by C(4) photosynthesis. It has been estimated that transferring the C(4) pathway to C(3) crops could boost yield by 50% and also increase water use efficiency and reduce the need for fertilizer, particularly in dry, hot environments. The high productivity of maize (Zea mays), sugarcane (Saccharum spp.) and several emerging bioenergy grasses is due largely to C(4) photosynthesis, which is enabled by the orderly arrangement, in concentric rings, of specialized bundle sheath and mesophyll cells in leaves in a pattern known as Kranz anatomy. Here we show that PIN, the auxin efflux protein, is present in the end walls of maize bundle sheath cells, as it is in the endodermis of the root. Since this marker suggests the expression of endodermal genetic programs in bundle sheath cells, we determined whether the transcription factor SCARECROW, which regulates structural differentiation of the root endodermis, also plays a role in the development of Kranz anatomy in maize. Mutations in the Scarecrow gene result in proliferation of bundle sheath cells, abnormal differentiation of bundle sheath chloroplasts, vein disorientation, loss of minor veins and reduction of vein density. Further characterization of this signal transduction pathway should facilitate the transfer of the C(4) trait into C(3) crop species, including rice.
Collapse
|
24
|
Morais de Sousa S, Clark RT, Mendes FVF, Carlos de Oliveira A, Vila A de Vasconcelos MJ, Parentoni SN, Kochian LV, Guimar Es CUT, Magalh Es JV. A role for root morphology and related candidate genes in P acquisition efficiency in maize. FUNCTIONAL PLANT BIOLOGY : FPB 2012; 39:925-935. [PMID: 32480842 DOI: 10.1071/fp12022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 05/28/2012] [Indexed: 05/10/2023]
Abstract
Phosphorus (P) is an essential nutrient for plants and is acquired from the rhizosphere solution as inorganic phosphate. P is one of the least available mineral nutrients, particularly in highly weathered, tropical soils, and can substantially limit plant growth. The aim of this work was to study a possible effect of root morphology and the expression pattern of related candidate genes on P efficiency in maize. Our field phenotyping results under low and high P conditions enabled us to identify two contrasting genotypes for P acquisition efficiency that were used for the root traits studies. Root morphology was assessed in a paper pouch system to investigate root traits that could be involved in P acquisition efficiency. The genes, Rtcs, Bk2 and Rth3, which are known to be involved in root morphology, showed higher expression in the P efficient line relative to the P inefficient line. Overall, root traits showed high heritability and a low coefficient of variation. Principal component analysis revealed that out of the 24 root traits analysed, only four root traits were needed to adequately represent the diversity among genotypes. The information generated by this study will be useful for establishing early selection strategies for P efficiency in maize, which are needed to support subsequent molecular and physiological studies.
Collapse
Affiliation(s)
| | - Randy T Clark
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, New York 14853-2901, USA
| | | | | | | | | | - Leon V Kochian
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, New York 14853-2901, USA
| | | | | |
Collapse
|
25
|
GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signalling. Biochem J 2012; 442:1-12. [PMID: 22280012 DOI: 10.1042/bj20111766] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
IDPs (intrinsically disordered proteins) are highly abundant in eukaryotic proteomes and important for cellular functions, especially in cell signalling and transcriptional regulation. An IDR (intrinsically disordered region) within an IDP often undergoes disorder-to-order transitions upon binding to various partners, allowing an IDP to recognize and bind different partners at various binding interfaces. Plant-specific GRAS proteins play critical and diverse roles in plant development and signalling, and act as integrators of signals from multiple plant growth regulatory and environmental inputs. Possessing an intrinsically disordered N-terminal domain, the GRAS proteins constitute the first functionally required unfoldome from the plant kingdom. Furthermore, the N-terminal domains of GRAS proteins contain MoRFs (molecular recognition features), short interaction-prone segments that are located within IDRs and are able to recognize their interacting partners by undergoing disorder-to-order transitions upon binding to these specific partners. These MoRFs represent potential protein-protein binding sites and may be acting as molecular bait in recognition events during plant development. Intrinsic disorder provides GRAS proteins with a degree of binding plasticity that may be linked to their functional versatility. As an overview of structure-function relationships for GRAS proteins, the present review covers the main biological functions of the GRAS family, the IDRs within these proteins and their implications for understanding mode-of-action.
Collapse
|
26
|
Pauluzzi G, Divol F, Puig J, Guiderdoni E, Dievart A, Périn C. Surfing along the root ground tissue gene network. Dev Biol 2012; 365:14-22. [PMID: 22349629 DOI: 10.1016/j.ydbio.2012.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 01/31/2012] [Accepted: 02/06/2012] [Indexed: 11/19/2022]
Abstract
Organization of tissues in Arabidopsis thaliana root is made of, from outside in, epidermis, cortex, middle cortex, endodermis, pericycle and vascular tissues. Cortex, middle cortex and endodermis form the ground tissue (GT) system. Functional and molecular characterization of GT patterning mutants' properties has greatly increased our understanding of fundamental processes of plant root development. These studies have demonstrated GT is an elegant model that can be used to study how different cell types and cell fates are specified. This review analyzes GT mutants to provide a detailed account of the molecular network that regulates GT formation in A. thaliana. The most recent results indicate an unexpectedly complex network of transcription factors, epigenetic and hormonal controls that play crucial roles in GT development. Major differences exist between GT formation in dicots and monocots, particularly in the model plant rice, opening the way for evo-devo of GT formation in angiosperm. In rice, adaptation to submergence relies on a multilayered cortex. Moreover, variation in the number of cortex cell layers is also observed between the five root types. A mechanism of control for cortical cell number should then exist in rice and it remains to be determined if any of the Arabidopsis thaliana identified GT network members are also involved in this process in rice. Alternatively, a totally different network may have been invented. However, first available results suggest functional conservation in rice of at least two transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR), involved in ground tissue formation in Arabidopsis.
Collapse
Affiliation(s)
- G Pauluzzi
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | | | | | | | | | | |
Collapse
|
27
|
Schlögl PS, Dos Santos ALW, Vieira LDN, Floh EIS, Guerra MP. Cloning and expression of embryogenesis-regulating genes in Araucaria angustifolia (Bert.) O. Kuntze (Brazilian Pine). Genet Mol Biol 2012; 35:172-81. [PMID: 22481892 PMCID: PMC3313508 DOI: 10.1590/s1415-47572012005000005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 08/27/2011] [Indexed: 11/22/2022] Open
Abstract
Angiosperm and gymnosperm plants evolved from a common ancestor about 300 million years ago. Apart from morphological and structural differences in embryogenesis and seed origin, a set of embryogenesis-regulating genes and the molecular mechanisms involved in embryo development seem to have been conserved alike in both taxa. Few studies have covered molecular aspects of embryogenesis in the Brazilian pine, the only economically important native conifer in Brazil. Thus eight embryogenesis-regulating genes, viz., ARGONAUTE 1, CUP-SHAPED COTYLEDON 1, WUSCHEL-related WOX, S-LOCUS LECTIN PROTEIN KINASE, SCARECROW-like, VICILIN 7S, LEAFY COTYLEDON 1, and REVERSIBLE GLYCOSYLATED POLYPEPTIDE 1, were analyzed through semi-quantitative RT-PCR during embryo development and germination. All the eight were found to be differentially expressed in the various developmental stages of zygotic embryos, seeds and seedling tissues. To our knowledge, this is the first report on embryogenesis-regulating gene expression in members of the Araucariaceae family, as well as in plants with recalcitrant seeds.
Collapse
Affiliation(s)
- Paulo Sérgio Schlögl
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | | | | | | |
Collapse
|
28
|
Lau S, Slane D, Herud O, Kong J, Jürgens G. Early embryogenesis in flowering plants: setting up the basic body pattern. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:483-506. [PMID: 22224452 DOI: 10.1146/annurev-arplant-042811-105507] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Early embryogenesis is the critical developmental phase during which the basic features of the plant body are established: the apical-basal axis of polarity, different tissue layers, and both the root pole and the shoot pole. Polarization of the zygote correlates with the generation of apical and basal (embryonic and extraembryonic) cell fates. Whereas mechanisms of zygote polarization are still largely unknown, distinct expression domains of WOX family transcription factors as well as directional auxin transport and local auxin response are known to be involved in early apical-basal patterning. Radial patterning of tissue layers appears to be mediated by cell-cell communication involving both peptide signaling and transcription factor movement. Although the initiation of the shoot pole is still unclear, the apical organization of the embryo depends on both the proper establishment of transcription factor expression domains and, for cotyledon initiation, upward auxin flow in the protoderm. Here we focus on the essential patterning processes, drawing mainly on data from Arabidopsis thaliana and also including relevant data from other species if available.
Collapse
Affiliation(s)
- Steffen Lau
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | | | | |
Collapse
|
29
|
Vielba JM, Díaz-Sala C, Ferro E, Rico S, Lamprecht M, Abarca D, Ballester A, Sánchez C. CsSCL1 is differentially regulated upon maturation in chestnut microshoots and is specifically expressed in rooting-competent cells. TREE PHYSIOLOGY 2011; 31:1152-60. [PMID: 21964478 DOI: 10.1093/treephys/tpr086] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Castanea sativa SCL1 gene (CsSCL1) has previously been shown to be induced by auxin during adventitious root (AR) formation in rooting-competent microshoots. However, its expression has not previously been analyzed in rooting-incompetent shoots. This study focuses on the regulation of CsSCL1 during maturation and the role of the gene in the formation of AR. The expression of CsSCL1 in rooting-incompetent microshoots and other tissues was investigated by quantitative reverse transcriptase--polymerase chain reaction. The analysis was complemented by in situ hybridization of the basal segments of rooting-competent and --incompetent microshoots during AR induction, as well as in AR and lateral roots. It was found that CsSCL1 is upregulated by auxin in a cell-type- and phase-dependent manner during the induction of AR. In root-forming shoots, CsSCL1 mRNA was specifically located in the cambial zone and derivative cells, which are rooting-competent cells, whereas in rooting-incompetent shoots the hybridization signal was more diffuse and evenly distributed through the phloem and parenchyma. CsSCL1 expression was also detected in lateral roots and axillary buds. The different CsSCL1 expression patterns in rooting-competent and -incompetent microshoots, together with the specific location of transcripts in cell types involved in root meristem initiation and in the root primordia of AR and lateral roots, indicate an important role for the gene in determining whether certain cells will enter the root differentiation pathway and its involvement in meristem maintenance.
Collapse
Affiliation(s)
- Jesús M Vielba
- Department of Plant Physiology, Instituto de Investigaciones Agrobiológicas de Galicia (IIAG-CSIC), Apartado 122, 15780 Santiago de Compostela, Spain
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Li W, Wu J, Weng S, Zhang Y, Zhang D, Shi C. Identification and characterization of dwarf 62, a loss-of-function mutation in DLT/OsGRAS-32 affecting gibberellin metabolism in rice. PLANTA 2010; 232:1383-96. [PMID: 20830595 DOI: 10.1007/s00425-010-1263-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/25/2010] [Indexed: 05/15/2023]
Abstract
A dwarf mutant, dwarf 62 (d62), was isolated from rice cultivar 93-11 by mutagenesis with γ-rays. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as dwarfism, wide and dark-green leaf blades, reduced tiller numbers, late and asynchronous heading, short roots, partial male sterility, etc. Genetic analysis indicated that the abnormal phenotypes were controlled by the recessive mutation of a single nuclear gene. Using molecular markers, the D62 gene was fine mapped in 131-kb region at the short arm of chromosome 6. Positional cloning of D62 gene revealed that it was the same locus as DLT/OsGRAS-32, which encodes a member of the GRAS family. In previous studies, the DLT/OsGRAS-32 is confirmed to play positive roles in brassinosteroid (BR) signaling. Sequence analysis showed that the d62 carried a 2-bp deletion in ORF region of D62 gene which led to a loss-of-function mutation. The function of D62 gene was confirmed by complementation experiment. RT-PCR analysis and promoter activity analysis showed that the D62 gene expressed in all tested tissues including roots, stems, leaves and panicles of rice plant. The d62 mutant exhibited decreased activity of α-amylase in endosperm and reduced content of endogenous GA(1). The expression levels of gibberellin (GA) biosynthetic genes including OsCPS1, OsKS1, OsKO1, OsKAO, OsGA20ox2/SD1 and OsGA2ox3 were significantly increased in d62 mutant. Briefly, these results demonstrated that the D62 (DLT/OsGRAS-32) not only participated in the regulation of BR signaling, but also influenced GA metabolism in rice.
Collapse
Affiliation(s)
- Wenqiang Li
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China
| | | | | | | | | | | |
Collapse
|
31
|
Marcon C, Schützenmeister A, Schütz W, Madlung J, Piepho HP, Hochholdinger F. Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development. J Proteome Res 2010; 9:6511-22. [PMID: 20973536 DOI: 10.1021/pr100718d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.
Collapse
Affiliation(s)
- Caroline Marcon
- Department of General Genetics, University of Tuebingen, ZMBP, Center for Plant Molecular Biology, 72076 Tuebingen, Germany
| | | | | | | | | | | |
Collapse
|
32
|
Sbabou L, Bucciarelli B, Miller S, Liu J, Berhada F, Filali-Maltouf A, Allan D, Vance C. Molecular analysis of SCARECROW genes expressed in white lupin cluster roots. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:1351-63. [PMID: 20167612 PMCID: PMC2837254 DOI: 10.1093/jxb/erp400] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 12/18/2009] [Accepted: 12/24/2009] [Indexed: 05/21/2023]
Abstract
The Scarecrow (SCR) transcription factor plays a crucial role in root cell radial patterning and is required for maintenance of the quiescent centre and differentiation of the endodermis. In response to phosphorus (P) deficiency, white lupin (Lupinus albus L.) root surface area increases some 50-fold to 70-fold due to the development of cluster (proteoid) roots. Previously it was reported that SCR-like expressed sequence tags (ESTs) were expressed during early cluster root development. Here the cloning of two white lupin SCR genes, LaSCR1 and LaSCR2, is reported. The predicted amino acid sequences of both LaSCR gene products are highly similar to AtSCR and contain C-terminal conserved GRAS family domains. LaSCR1 and LaSCR2 transcript accumulation localized to the endodermis of both normal and cluster roots as shown by in situ hybridization and gene promoter::reporter staining. Transcript analysis as evaluated by quantitative real-time-PCR (qRT-PCR) and RNA gel hybridization indicated that the two LaSCR genes are expressed predominantly in roots. Expression of LaSCR genes was not directly responsive to the P status of the plant but was a function of cluster root development. Suppression of LaSCR1 in transformed roots of lupin and Medicago via RNAi (RNA interference) delivered through Agrobacterium rhizogenes resulted in decreased root numbers, reflecting the potential role of LaSCR1 in maintaining root growth in these species. The results suggest that the functional orthologues of AtSCR have been characterized.
Collapse
Affiliation(s)
- Laila Sbabou
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108, USA
- Laboratoire de Microbiologie et Biologie Moléculaire, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bruna Bucciarelli
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St Paul, MN 55108, USA
| | - Susan Miller
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St Paul, MN 55108, USA
| | - Junqi Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108, USA
| | - Fatiha Berhada
- Laboratoire de Microbiologie et Biologie Moléculaire, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratoire de Microbiologie et Biologie Moléculaire, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Deborah Allan
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108, USA
| | - Carroll Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108, USA
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St Paul, MN 55108, USA
| |
Collapse
|
33
|
Muthreich N, Schützenmeister A, Schütz W, Madlung J, Krug K, Nordheim A, Piepho HP, Hochholdinger F. Regulation of the maize (Zea mays L.) embryo proteome by RTCS which controls seminal root initiation. Eur J Cell Biol 2010; 89:242-9. [DOI: 10.1016/j.ejcb.2009.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
|
34
|
Saleem M, Lamkemeyer T, Schützenmeister A, Fladerer C, Piepho HP, Nordheim A, Hochholdinger F. Tissue Specific Control of the Maize (Zea mays L.) Embryo, Cortical Parenchyma, and Stele Proteomes by RUM1 Which Regulates Seminal and Lateral Root Initiation. J Proteome Res 2009; 8:2285-97. [DOI: 10.1021/pr8009287] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Muhammad Saleem
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Tobias Lamkemeyer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - André Schützenmeister
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Claudia Fladerer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Hans-Peter Piepho
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Alfred Nordheim
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Frank Hochholdinger
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| |
Collapse
|
35
|
Hochholdinger F, Zimmermann R. Conserved and diverse mechanisms in root development. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:70-4. [PMID: 18006363 DOI: 10.1016/j.pbi.2007.10.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 09/28/2007] [Accepted: 10/02/2007] [Indexed: 05/19/2023]
Abstract
The molecular basis of root formation and growth is being analyzed in more and more detail in the dicot model organism Arabidopsis. However, considerable progress has also been made in the molecular and genetic dissection of root system development in the monocot species rice and maize. This review will highlight some recent molecular data that allow for the comparison of cereal and Arabidopsis root development. Members of the COBRA, GRAS, and LOB domain gene families and a gene encoding a subunit of the exocyst complex are associated with root development. Analyses of these genes revealed some common and distinct molecular principles and functions in cereal versus Arabidopsis root formation.
Collapse
Affiliation(s)
- Frank Hochholdinger
- University of Tuebingen, Center for Plant Molecular Biology (ZMBP), Department of General Genetics, Auf der Morgenstelle 28, 72076 Tuebingen, Germany.
| | | |
Collapse
|
36
|
|
37
|
Identification and sequencing of ESTs from the halophyte grass Aeluropus littoralis. Gene 2007; 404:61-9. [PMID: 17916418 DOI: 10.1016/j.gene.2007.08.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 08/17/2007] [Accepted: 08/29/2007] [Indexed: 11/23/2022]
Abstract
Aeluropus littoralis (Gouan) Parl. is a C4 perennial halophyte monocotyledonous plant belonging to the same family as wheat. Growing as weed in dry salty areas or marshes, it is salt-secreting, rhizomatous and is used as forage. It is diploid (2n=2X=14) and has a relative small genome of around 342 Mb. A. littoralis is highly salt-tolerant since this plant has the ability to secrete salt. Thus, A. littoralis has the potential to become an important genetic resource for biotechnological strategies to improve salt and drought tolerance in economically important crops such as wheat. We have constructed SSH (Suppression Subtractive Hybridization) cDNA libraries from root (RSD45) and leaf (LSD45) tissues of 45 days old plants grown in the presence of 300 mM NaCl. We have also constructed full-length cDNA library from 15 days old salt stressed (300 mM NaCl) roots (RSTL15). Sequencing revealed 25 and 42 independent transcripts from the RSD45 and LSD45 cDNA libraries respectively, in both cases this was less than 25% of the clones sequenced. In contrast, 425 (60%) of the clones from the RSTL15 library revealed independent transcripts. After comparison with protein databases using BlastX, 335 (68%) ESTs (Expressed Sequence Tag) were classified into putative known functions and unclassified proteins, 59 (12%) have homology only to unidentified homologous sequences. A total of 98 (20%) of the ESTs have no homologies to known sequences in the protein databases which can be considered as novel.
Collapse
|
38
|
Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 2007; 316:421-5. [PMID: 17446396 DOI: 10.1126/science.1139531] [Citation(s) in RCA: 375] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Intercellular protein movement plays a critical role in animal and plant development. SHORTROOT (SHR) is a moving transcription factor essential for endodermis specification in the Arabidopsis root. Unlike diffusible animal morphogens, which form a gradient across multiple cell layers, SHR movement is limited to essentially one cell layer. However, the molecular mechanism is unknown. We show that SCARECROW (SCR) blocks SHR movement by sequestering it into the nucleus through protein-protein interaction and a safeguard mechanism that relies on a SHR/SCR-dependent positive feedback loop for SCR transcription. Our studies with SHR and SCR homologs from rice suggest that this mechanism is evolutionarily conserved, providing a plausible explanation why nearly all plants have a single layer of endodermis.
Collapse
Affiliation(s)
- Hongchang Cui
- Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Laajanen K, Vuorinen I, Salo V, Juuti J, Raudaskoski M. Cloning of Pinus sylvestris SCARECROW gene and its expression pattern in the pine root system, mycorrhiza and NPA-treated short roots. THE NEW PHYTOLOGIST 2007; 175:230-243. [PMID: 17587372 DOI: 10.1111/j.1469-8137.2007.02102.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The SCARECROW (SCR) gene is central to root radial patterning. Its expression has not been investigated in conifers with morphologically different root types. Additional interest in SCR functions in the Pinus sylvestris root system comes from the effect of ectomycorrhiza formation on the short root apical structure. Here, the P. sylvestris SCR gene (PsySCR) was cloned and its expression investigated by northern blot and in situ hybridization of primary, lateral and short roots and mycorrhiza. Short root dichotomization was induced by auxin transport inhibitor (N-1-naphthylphthalamic acid (NPA)). PsySCR has conserved GRAS family protein motifs at the C-terminus and a variable N-terminus. PsySCR expression occurred in young root tissue and mycorrhiza. In root sections the PsySCR signal runs through the tip in initials for stele and root cap column and becomes upwards-restricted to endodermis in all root types. The PsySCR expression pattern suggests for the first time a regulatory role for SCR in maintaining the endodermal characteristics and radial patterning of roots with open meristem organization. The specific PsySCR localization is also an excellent marker for investigation of the dichotomization process in short roots.
Collapse
Affiliation(s)
- Kaisa Laajanen
- Plant Biology, Department of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Irmeli Vuorinen
- Plant Biology, Department of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Vanamo Salo
- Plant Biology, Department of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
- Botany, Department of Applied Biology, University of Helsinki, FI-00014 University of Helsinki, Finland
| | - Jarmo Juuti
- General Microbiology, Department of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Marjatta Raudaskoski
- Plant Physiology and Molecular Biology, Department of Biology, FI-20014 University of Turku, Finland
| |
Collapse
|
40
|
Woll K, Dressel A, Sakai H, Piepho HP, Hochholdinger F. ZmGrp3: identification of a novel marker for root initiation in maize and development of a robust assay to quantify allele-specific contribution to gene expression in hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1305-15. [PMID: 16937154 DOI: 10.1007/s00122-006-0384-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 07/31/2006] [Indexed: 05/11/2023]
Abstract
This study comprises a comprehensive gene expression analysis of the root tip specific maize gene ZmGrp3. In the first part of this paper expression of ZmGrp3 was studied in maize inbred lines. First, RNA in situ hybridization experiments confined the expression of ZmGrp3 to the columella and the epidermis of all embryonic and postembryonic root types. Second, Northern-blot analyses of the maize root initiation mutants rtcs and lrt1 revealed that the ZmGrp3 gene is not expressed prior to root initiation, thus providing a novel marker for this developmental process. Finally, a comprehensive expression profiling in 42 tissues via the Lynx MPSS system revealed almost exclusive expression of ZmGrp3 in maize roots. In the second part of this survey, ZmGrp3 expression was assayed in maize hybrids. In this context, a novel approach to quantify allele-specific contribution to gene expression in maize hybrids was developed. This assay combines RT-PCR amplification of polymorphisms between two alleles and subsequent quantification of allele-specific gene expression via a combination of didesoxyterminator assays and capillary electrophoresis. Allelic expression of the ZmGrp3 gene in six reciprocal hybrids generated from three ZmGrp3 alleles was analyzed via a new statistical mixed model approach.
Collapse
Affiliation(s)
- Katrin Woll
- Center for Plant Molecular Biology (ZMBP), Department of General Genetics, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 28, Tuebingen 72076, Germany
| | | | | | | | | |
Collapse
|
41
|
Sauer M, Jakob A, Nordheim A, Hochholdinger F. Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.). Proteomics 2006; 6:2530-41. [PMID: 16521151 DOI: 10.1002/pmic.200500564] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Postembryonically formed shoot-borne roots make up the major backbone of the adult maize root stock. In this study the abundant soluble proteins of the first node (coleoptilar node) of wild-type and mutant rtcs seedlings, which do not initiate crown roots, were compared at two early stages of crown root formation. In Coomassie Bluestained 2-D gels, representing soluble proteins of coleoptilar nodes 5 and 10 days after germination, 146 and 203 proteins were detected, respectively. Five differentially accumulated proteins (> two-fold change; t-test: 95% significance) were identified in 5-day-old and 14 differentially accumulated proteins in 10-day-old coleoptilar nodes of wild-type versus rtcs. All 19 differentially accumulated proteins were identified via ESI MS/MS mass spectrometry. Five differentially accumulated proteins, including a regulatory G-protein and a putative auxin-binding protein, were further analyzed at the RNA expression level. These experiments confirmed differential gene expression and revealed subtle developmental regulation of these genes during early coleoptilar node development. This study represents the first proteomic analysis of shoot-borne root initiation in cereals and will contribute to a better understanding of the molecular basis of this developmental process unique to cereals.
Collapse
Affiliation(s)
- Michaela Sauer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, Tuebingen, Germany
| | | | | | | |
Collapse
|
42
|
Zeng F, Zhang X, Zhu L, Tu L, Guo X, Nie Y. Isolation and characterization of genes associated to cotton somatic embryogenesis by suppression subtractive hybridization and macroarray. PLANT MOLECULAR BIOLOGY 2006; 60:167-83. [PMID: 16429258 DOI: 10.1007/s11103-005-3381-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Accepted: 09/22/2005] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis (SE) is the developmental reprogramming of somatic cells toward the embryogenesis pathway and is a notable illustration of cell totipotency. To identify genes involved in SE, subtractive polymerase chain reaction (PCR) was performed to generate transcripts highly enriched for SE-related genes, using cDNA prepared from a mixture of embryogenic callus and pre-globular somatic embryos, as the tester, and cDNA from non-embryogenic callus, as the driver. After differential screening and subsequent confirmation by reverse Northern blot analysis, a total of 671 differentially expressed cDNA fragments were identified, and 242 uni-genes significantly up-regulated during cotton SE were recovered, as confirmed by Northern blot and reverse-transcription PCR analysis of representative cases, including most previously published SE-related genes in plants. In total, more than half had not been identified previously as SE-related genes, including dominant crucial genes involved in transcription, post-transcription, and transportation, and about one-third had not been reported previously to GenBank or were expected to be unknown, or newly identified genes. We used cDNA arrays to further investigate the expression patterns of these genes in differentiating gradient culture, ranging from pro-embryogenic masses to somatic embryos at every stage. The cDNA collection is composed of a broad repertoire of SE genes which is an important resource for understanding the genetic interactions underlying SE signaling and regulation. Our results suggested that a complicated and concerted mechanism involving multiple cellular pathways is responsible for cotton SE. This report represents a systematic and comprehensive analysis of genes involved in the process of somatic embryogenesis.
Collapse
Affiliation(s)
- Fanchang Zeng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | | | | | | | | | | |
Collapse
|
43
|
Woll K, Borsuk LA, Stransky H, Nettleton D, Schnable PS, Hochholdinger F. Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1. PLANT PHYSIOLOGY 2005; 139:1255-67. [PMID: 16215225 PMCID: PMC1283763 DOI: 10.1104/pp.105.067330] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The monogenic recessive maize (Zea mays) mutant rootless with undetectable meristems 1 (rum1) is deficient in the initiation of the embryonic seminal roots and the postembryonic lateral roots at the primary root. Lateral root initiation at the shoot-borne roots and development of the aerial parts of the mutant rum1 are not affected. The mutant rum1 displays severely reduced auxin transport in the primary root and a delayed gravitropic response. Exogenously applied auxin does not induce lateral roots in the primary root of rum1. Lateral roots are initiated in a specific cell type, the pericycle. Cell-type-specific transcriptome profiling of the primary root pericycle 64 h after germination, thus before lateral root initiation, via a combination of laser capture microdissection and subsequent microarray analyses of 12k maize microarray chips revealed 90 genes preferentially expressed in the wild-type pericycle and 73 genes preferentially expressed in the rum1 pericycle (fold change >2; P-value <0.01; estimated false discovery rate of 13.8%). Among the 51 annotated genes predominately expressed in the wild-type pericycle, 19 genes are involved in signal transduction, transcription, and the cell cycle. This analysis defines an array of genes that is active before lateral root initiation and will contribute to the identification of checkpoints involved in lateral root formation downstream of rum1.
Collapse
Affiliation(s)
- Katrin Woll
- Center for Plant Molecular Biology, Department of General Genetics , Eberhard Karls University, 72076 Tuebingen, Germany
| | | | | | | | | | | |
Collapse
|
44
|
Abstract
The establishment of the Angiosperm root apical meristem is dependent on the specification of a stem cell niche and the subsequent development of the quiescent center at the presumptive root pole. Distribution of auxin and the establishment of auxin maxima are early formative steps in niche specification that depend on the expression and distribution of auxin carriers. Auxin specifies stem cell niche formation by directly and indirectly affecting gene activities. Part of the indirect regulation by auxin may involve changes in redox, favoring local, oxidized microenvironments. Formation of a QC is required for root meristem development and elaboration. Many signals likely pass between the QC and the adjacent root meristem tissues. Disappearance of the QC is associated with roots becoming determinate. Given the many auxin feedback loops, we hypothesize that roots evolved as part of an auxin homeostasis mechanism.
Collapse
Affiliation(s)
- Keni Jiang
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
| | | |
Collapse
|
45
|
Lim J, Jung JW, Lim CE, Lee MH, Kim BJ, Kim M, Bruce WB, Benfey PN. Conservation and diversification of SCARECROW in maize. PLANT MOLECULAR BIOLOGY 2005; 59:619-30. [PMID: 16244911 PMCID: PMC1475827 DOI: 10.1007/s11103-005-0578-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Accepted: 07/05/2005] [Indexed: 05/05/2023]
Abstract
The SCARECROW (SCR) gene in Arabidopsis is required for asymmetric cell divisions responsible for ground tissue formation in the root and shoot. Previously, we reported that Zea mays SCARECROW (ZmSCR) is the likely maize ortholog of SCR. Here we describe conserved and divergent aspects of ZmSCR. Its ability to complement the Arabidopsis scr mutant phenotype suggests conservation of function, yet its expression pattern during embryogenesis and in the shoot system indicates divergence. ZmSCR expression was detected early during embryogenesis and localized to the endodermal lineage in the root, showing a gradual regionalization of expression. Expression of ZmSCR appeared to be analogous to that of SCR during leaf formation. However, its absence from the maize shoot meristem and its early expression pattern during embryogenesis suggest a diversification of ZmSCR in the patterning processes in maize. To further investigate the evolutionary relationship of SCR and ZmSCR, we performed a phylogenetic analysis using Arabidopsis, rice and maize SCARECROW-LIKE genes (SCLs). We found SCL23 to be the most closely related to SCR in both eudicots and monocots, suggesting that a gene duplication resulting in SCR and SCL23 predates the divergence of dicots and monocots.
Collapse
Affiliation(s)
- Jun Lim
- Department of Molecular Biotechnology, Konkuk University, 143-701 Seoul, Korea.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Zimmermann R, Werr W. Pattern formation in the monocot embryo as revealed by NAM and CUC3 orthologues from Zea mays L. PLANT MOLECULAR BIOLOGY 2005; 58:669-85. [PMID: 16158242 DOI: 10.1007/s11103-005-7702-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Accepted: 05/21/2005] [Indexed: 05/04/2023]
Abstract
All aerial parts of a higher plant originate from the shoot apical meristem (SAM), which is initiated during embryogenesis as a part of the basic body plan. In contrast to dicot species, the SAM in Zea mays is not established at an apico-central, but at a lateral position of the transition stage embryo. Genetic and molecular studies in dicots have revealed that members of the NAC gene family of plant-specific transcription factors such as NO APICAL MERISTEM (NAM) from Petunia or the CUP-SHAPED COTYLEDON (CUC) genes from Arabidopsis contribute essential functions to the establishment of the SAM and cotyledon separation. As an approach to the understanding of meristem formation in a monocot species, members of the maize NAC family highly related to the NAM/CUC genes were isolated and characterized. Our phylogenetic analysis indicates that two distinct NAM and CUC3 precursors already existed prior to the separation of mono- and dicot species. The allocation of the two maize paralogues, ZmNAM1 and ZmNAM2 together with PhNAM, AtCUC2 and AmCUP in one sub-branch and the corresponding expression patterns support their contribution to SAM establishment. In contrast, the ZmCUC3 orthologue is associated with boundary specification at the SAM periphery, where it visualizes which fraction of cells in the SAM is committed to a new leaf primordium. Other maize NAC gene family members are clearly positioned outside of this NAM/CUC3 branch and also exhibit highly cell type-specific expression patterns.
Collapse
Affiliation(s)
- Roman Zimmermann
- Institut für Entwicklungsbiologie, Gyrhofstr. 17, D-50923, Köln, Germany
| | | |
Collapse
|
47
|
Terauchi K, Asakura T, Nishizawa NK, Matsumoto I, Abe K. Characterization of the genes for two soybean aspartic proteinases and analysis of their different tissue-dependent expression. PLANTA 2004; 218:947-57. [PMID: 14727111 DOI: 10.1007/s00425-003-1179-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2003] [Accepted: 11/06/2003] [Indexed: 05/24/2023]
Abstract
We isolated and characterized two cDNAs for aspartic proteinases (APs; EC 3.4.23) in soybean [Glycine max (L.) Merr.]. The encoded enzymes, soyAP1 and soyAP2, share 55% amino acid sequence identity. Northern analysis demonstrated that soyAP1 is expressed specifically in seeds, especially in dry seeds, while the expression of soyAP2 takes place in various tissues such as roots, stems, leaves and flowers, but not in dry seeds. SoyAP1 is highly expressed even at an early stage of germination, with a subsequent decrease in expression intensity. In contrast, the soyAP2 mRNA level increases 48 h after imbibition. To elucidate the physiological functions of soyAPs, we investigated the localization of soyAP expression in seeds germinating for 48 h at 25 degrees C. SoyAP1 shows cell-type-specific expression in sieve tube cells of the hypocotyl. At the root tip, soyAP1 is expressed in immature tracheary elements and sieve tube cells, and its expression pattern changes with distance from the tip; strong signals observed throughout phloem converge gradually to sieve tube cells, whereas those observed in tracheary elements disappear while the elements are still immature. On the other hand, soyAP2 signals were detected broadly in the boundary region between the cortex and the central cylinder. These results suggest that soyAP1 and soyAP2 are functionally different from each other.
Collapse
Affiliation(s)
- Kaede Terauchi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657 Tokyo, Japan
| | | | | | | | | |
Collapse
|
48
|
Tian C, Wan P, Sun S, Li J, Chen M. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. PLANT MOLECULAR BIOLOGY 2004; 54:519-32. [PMID: 15316287 DOI: 10.1023/b:plan.0000038256.89809.57] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Members of the GRAS gene family encode transcriptional regulators that have diverse functions in plant growth and development such as gibberellin signal transduction, root radial patterning, axillary meristem formation, phytochrome A signal transduction, and gametogenesis. Bioinformatic analysis identified 57 and 32 GRAS genes in rice and Arabidopsis, respectively. Here, we provide a complete overview of this gene family, describing the gene structure, gene expression, chromosome localization, protein motif organization, phylogenetic analysis, and comparative analysis between rice and Arabidopsis. Phylogenetic analysis divides the GRAS gene family into eight subfamilies, which have distinct conserved domains and functions. Both genome/segmental duplication and tandem duplication contributed to the expansion of the GRAS gene family in the rice and Arabidopsis genomes. The existence of GRAS-like genes in bryophytes suggests that GRAS is an ancient family of transcription factors, which arose before the appearance of land plants over 400 million years ago.
Collapse
Affiliation(s)
- Chaoguang Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China
| | | | | | | | | |
Collapse
|
49
|
Bolle C. The role of GRAS proteins in plant signal transduction and development. PLANTA 2004; 218:683-92. [PMID: 14760535 DOI: 10.1007/s00425-004-1203-z] [Citation(s) in RCA: 325] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2003] [Accepted: 12/29/2003] [Indexed: 05/18/2023]
Abstract
GRAS proteins are a recently discovered family of plant-specific proteins named after GAI, RGA and SCR, the first three of its members isolated. Although the Arabidopsis genome encodes at least 33 GRAS protein family members only a few GRAS proteins have been characterized so far. However, it is becoming clear that GRAS proteins exert important roles in very diverse processes such as signal transduction, meristem maintenance and development. Here we present a survey of the different GRAS proteins and review the current knowledge of the function of individual members of this protein family.
Collapse
Affiliation(s)
- Cordelia Bolle
- Department Biologie I, Bereich Botanik, Universität München, Menzinger Str 67, 80638, München, Germany.
| |
Collapse
|
50
|
Hochholdinger F, Park WJ, Sauer M, Woll K. From weeds to crops: genetic analysis of root development in cereals. TRENDS IN PLANT SCIENCE 2004; 9:42-8. [PMID: 14729218 DOI: 10.1016/j.tplants.2003.11.003] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Root development of Arabidopsis, Zea mays (maize) and Oryza sativa (rice) differs in both overall architecture and the anatomy of individual roots. In maize and rice, the post-embryonic shoot-borne root system becomes the major backbone of the root stock; in Arabidopsis, the embryonic root system formed by a simple primary root and its lateral roots remains dominant. Recently, several specific root mutants and root-specific genes have been identified and characterized in maize and rice. Interestingly, some of these mutants indicate that the formation of primary-, seminal-, crown- and lateral roots is regulated by alternative root-type-specific pathways. Further analyses of these unique pathways will contribute to the understanding of the complex molecular networks involved in cereal root formation.
Collapse
Affiliation(s)
- Frank Hochholdinger
- Center for Plant Molecular Biology, Department of General Genetics, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
| | | | | | | |
Collapse
|