1
|
Kumar A, Verma K, Kashyap R, Joshi VJ, Sircar D, Yadav SR. Auxin-responsive ROS homeostasis genes display dynamic expression pattern during rice crown root primordia morphogenesis. Plant Physiol Biochem 2024; 206:108307. [PMID: 38159549 DOI: 10.1016/j.plaphy.2023.108307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Reactive oxygen species (ROS) are generated continuously as a by-product of aerobic metabolism in plants. While excessive ROS cause oxidative stresses in cells, they act as signaling molecules when maintained at an optimum concentration through the dynamic equilibrium of ROS metabolizing mechanisms to regulate growth, development and response to environmental stress. Auxin and its crosstalk with other signaling cascades are crucial for maintaining ROS homeostasis and orchestrating root architecture but dissecting the underlying mechanism requires detailed investigation at the molecular level. Rice fibrous root system is primarily composed of shoot-derived adventitious roots (also called crown roots). Here, we uncover auxin-ROS cross-talk during initiation and growth of rice roots. Potassium iodide treatment changes ROS levels that results in an altered rice root architecture. We reveal that auxin induction recover root growth and development defects by recouping level of hydrogen peroxide. By comparing global datasets previously generated by auxin induction and laser capture microdissection-RNA sequencing, we identify the redox-related antioxidants genes from peroxidase, glutathione reductase, glutathione S-transferase, and thioredoxin reductase families whose expression is regulated by the auxin signaling and also display dynamic expression patterns during crown root primordia morphogenesis. The auxin-mediated differential transcriptome data were validated by quantifying expression levels of a set of genes upon auxin induction. Further, in-depth spatio-temporal expression pattern analysis by RNA in situ hybridization shows the spatially restricted expression of selected genes in the developing crown root primordia. Together, our findings uncover molecular components of auxin-ROS crosstalk involved in root organogenesis.
Collapse
Affiliation(s)
- Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Komal Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Rohan Kashyap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Vedika Jayant Joshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
| |
Collapse
|
2
|
Lee S, Tri Le Q, Yang S, Hwang KY, Lee H. Arabidopsis ecotype Ct-1, with its altered nitrate sensing ability, exhibits enhanced growth under low nitrate conditions in comparison to Col-0. Plant Sci 2023; 336:111827. [PMID: 37586419 DOI: 10.1016/j.plantsci.2023.111827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
To address the urgent need for sustainable solutions to the increased use of nitrogen fertilizers in agriculture, it is imperative to acquire an in-depth comprehension of the intricate interplay between plants and nitrogen. In this context, our research aimed to elucidate the molecular mechanism behind NO3- sensing/signaling in plants, which can enhance nitrogen utilization efficiency. Previous reports have revealed that the density and quantity of root hairs exhibit responsive behavior to varying levels of NO3-, while the precise molecular mechanisms governing these changes remain elusive. To further investigate this phenomenon, we specifically selected the Ct-1 ecotype, which manifested a greater abundance of root hairs compared to the Col-0 ecotype under conditions of low NO3-. Our investigations unveiled that the dissimilarities in the amino acid sequence of NRT1.1, a transceptor responsible for regulating nitrate signaling and transport, accounted for the observed variation in root hair numbers. These results suggest that NRT1.1 represents a promising target for gene editing technology, offering potential applications in enhancing the efficiency of nitrogen utilization in agricultural crops.
Collapse
Affiliation(s)
- Seokjin Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Quang Tri Le
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Seonyoung Yang
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Hojoung Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea.
| |
Collapse
|
3
|
Yang X, Poelmans W, Grones C, Lakehal A, Pevernagie J, Van Bel M, Njo M, Xu L, Nelissen H, De Rybel B, Motte H, Beeckman T. Spatial transcriptomics of a lycophyte root sheds light on root evolution. Curr Biol 2023; 33:4069-4084.e8. [PMID: 37683643 DOI: 10.1016/j.cub.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/15/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Plant roots originated independently in lycophytes and euphyllophytes, whereas early vascular plants were rootless. The organization of the root apical meristem in euphyllophytes is well documented, especially in the model plant Arabidopsis. However, little is known about lycophyte roots and their molecular innovations during evolution. In this study, spatial transcriptomics was used to detect 97 root-related genes in the roots of the lycophyte Selaginella moellendorffii. A high number of genes showed expression patterns similar to what has been reported for seed plants, supporting the idea of a highly convergent evolution of mechanisms to control root development. Interaction and complementation data of SHORTROOT (SHR) and SCARECROW (SCR) homologs, furthermore, support a comparable regulation of the ground tissue (GT) between euphyllophytes and lycophytes. Root cap formation, in contrast, appears to be differently regulated. Several experiments indicated an important role of the WUSCHEL-RELATED HOMEOBOX13 gene SmWOX13a in Selaginella root cap formation. In contrast to multiple Arabidopsis WOX paralogs, SmWOX13a is able to induce root cap cells in Arabidopsis and has functionally conserved homologs in the fern Ceratopteris richardii. Lycophytes and a part of the euphyllophytes, therefore, may share a common mechanism regulating root cap formation, which was diversified or lost during seed plant evolution. In summary, we here provide a new spatial data resource for the Selaginella root, which in general advocates for conserved mechanisms to regulate root development but shows a clear divergence in the control of root cap formation, with a novel putative role of WOX genes in root cap formation in non-seed plants.
Collapse
Affiliation(s)
- Xilan Yang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ward Poelmans
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Carolin Grones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Abdellah Lakehal
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Julie Pevernagie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Maria Njo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lin Xu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| |
Collapse
|
4
|
Uemura Y, Kimura S, Ohta T, Suzuki T, Mase K, Kato H, Sakaoka S, Uefune M, Komine Y, Hotta K, Shimizu M, Morikami A, Tsukagoshi H. A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis. Plant J 2023; 115:1408-1427. [PMID: 37247130 DOI: 10.1111/tpj.16330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.
Collapse
Affiliation(s)
- Yuta Uemura
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Saori Kimura
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Tomomichi Ohta
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan
| | - Kosuke Mase
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Kato
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Satomi Sakaoka
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Masayoshi Uefune
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Yuki Komine
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Kazuhiro Hotta
- Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Atsushi Morikami
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Hironaka Tsukagoshi
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan
| |
Collapse
|
5
|
Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, Martienssen RA. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. bioRxiv 2023:2023.08.24.554647. [PMID: 37662366 PMCID: PMC10473749 DOI: 10.1101/2023.08.24.554647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.
Collapse
Affiliation(s)
| | | | - Cristiane de Santis Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Laís Araujo Coelho
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Gil Eshel
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Samantha Frangos
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Katherine Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaojin Wang
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Yin Peng Lee
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Stella Loke
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Australian Botanic Garden, Mount Annan, NSW 2567, Australia
| | - Sebastiano Nigris
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Silvia Moschin
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Damon P. Little
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Manpreet S. Katari
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Kranthi Varala
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Barbara Ambrose
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Larry J. Croft
- School of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Gloria M. Coruzzi
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Michael Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| |
Collapse
|
6
|
Garg T, Yadav M, Mushahary KKK, Kumar A, Pal V, Singh H, Jain M, Yadav SR. Spatially activated conserved auxin-transcription factor regulatory module controls de novo root organogenesis in rice. Planta 2023; 258:52. [PMID: 37491477 DOI: 10.1007/s00425-023-04210-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
MAIN CONCLUSION This study reveals that the process of crown root development and auxin-induced de novo root organogenesis during in vitro plantlet regeneration share a common auxin-OsWOX10 regulatory module in rice. In the fibrous-type root system of rice, the crown roots (CR) are developed naturally from the shoot tissues. Generation of robust auxin response, followed by activation of downstream cell fate determinants and signaling pathways at the onset of crown root primordia (CRP) establishment is essential for new root initiation. During rice tissue culture, embryonic calli are induced to regenerate shoots in vitro which undergo de novo root organogenesis on an exogenous auxin-supplemented medium, but the mechanism underlying spatially restricted root organogenesis remains unknown. Here, we reveal the dynamics of progressive activation of genes involved in auxin homeostasis and signaling during initiation and outgrowth of rice crown root primordia. By comparative global dataset analysis, we identify the crown root primordia-expressed genes whose expression is also regulated by auxin signaling. In-depth spatio-temporal expression pattern analysis shows that the exogenous application of auxin induces a set of key transcription factors exclusively in the spatially positioned CRP. Further, functional analysis of rice WUSCHEL-RELATED HOMEOBOX 10 (OsWOX10) during in vitro plantlet regeneration from embryogenic calli shows that it promotes de novo root organogenesis from regenerated shoots. Expression of rice OsWOX10 also induces adventitious roots (AR) in Arabidopsis, independent of homologous endogenous Arabidopsis genes. Together, our findings reveal that a common auxin-transcription factor regulatory module is involved in root organogenesis under different conditions.
Collapse
Affiliation(s)
- Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Manoj Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Department of Biochemistry, All India Institute of Medical Sciences, Raebareli, Uttar Pradesh, India
| | | | - Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Vivek Pal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Center for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
| |
Collapse
|
7
|
Singh H, Singh Z, Kashyap R, Yadav SR. Lateral root branching: evolutionary innovations and mechanistic divergence in land plants. New Phytol 2023; 238:1379-1385. [PMID: 36882384 DOI: 10.1111/nph.18864] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
The root system architecture in plants is a result of multiple evolutionary innovations over time in response to changing environmental cues. Dichotomy and endogenous lateral branching in the roots evolved in lycophytes lineage but extant seed plants use lateral branching instead. This has led to the development of complex and adaptive root systems, with lateral roots playing a key role in this process exhibiting conserved and divergent features in different plant species. The study of lateral root branching in diverse plant species can shed light on the orderly yet distinct nature of postembryonic organogenesis in plants. This insight provides an overview of the diversity in lateral root (LR) development in various plant species during the evolution of root system in plants.
Collapse
Affiliation(s)
- Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
- Center for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Zeenu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Rohan Kashyap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| |
Collapse
|
8
|
Zhang M, Chen Y, Xing H, Ke W, Shi Y, Sui Z, Xu R, Gao L, Guo G, Li J, Xing J, Zhang Y. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize. J Integr Plant Biol 2023; 65:772-790. [PMID: 36354146 DOI: 10.1111/jipb.13408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.
Collapse
Affiliation(s)
- Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Agronomy College of Shandong Agricultural University, Taian, 271018, China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Yantai Science and Technology Innovation Promotion Center, Yantai, 264003, China
| | - Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganggang Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
9
|
García I, Chouaia B, Llabrés M, Simeoni M. Exploring the expressiveness of abstract metabolic networks. PLoS One 2023; 18:e0281047. [PMID: 36758030 PMCID: PMC9910719 DOI: 10.1371/journal.pone.0281047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Metabolism is characterised by chemical reactions linked to each other, creating a complex network structure. The whole metabolic network is divided into pathways of chemical reactions, such that every pathway is a metabolic function. A simplified representation of metabolism, which we call an abstract metabolic network, is a graph in which metabolic pathways are nodes and there is an edge between two nodes if their corresponding pathways share one or more compounds. The abstract metabolic network of a given organism results in a small network that requires low computational power to be analysed and makes it a suitable model to perform a large-scale comparison of organisms' metabolism. To explore the potentials and limits of such a basic representation, we considered a comprehensive set of KEGG organisms, represented through their abstract metabolic network. We performed pairwise comparisons using graph kernel methods and analyse the results through exploratory data analysis and machine learning techniques. The results show that abstract metabolic networks discriminate macro evolutionary events, indicating that they are expressive enough to capture key steps in metabolism evolution.
Collapse
Affiliation(s)
- Irene García
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Bessem Chouaia
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
| | - Mercè Llabrés
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Marta Simeoni
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
- European Centre for Living Technology (ECLT), Venice, Italy
- * E-mail:
| |
Collapse
|
10
|
Abstract
Xerobranching, a temporary suppression of root branching when water is limiting, is controlled by the plant hormone abscisic acid (ABA). A recently published study reveals how root branching is dynamically controlled by redistribution in opposite directions of ABA and auxin.
Collapse
Affiliation(s)
- Mingyuan Zhu
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
| |
Collapse
|
11
|
Li L, Zheng Q, Jiang W, Xiao N, Zeng F, Chen G, Mak M, Chen ZH, Deng F. Molecular Regulation and Evolution of Cytokinin Signaling in Plant Abiotic Stresses. Plant Cell Physiol 2023; 63:1787-1805. [PMID: 35639886 DOI: 10.1093/pcp/pcac071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/04/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of crops faces increasing challenges from global climate change and human activities, which leads to increasing instances of many abiotic stressors to plants. Among the abiotic stressors, drought, salinity and excessive levels of toxic metals cause reductions in global agricultural productivity and serious health risks for humans. Cytokinins (CKs) are key phytohormones functioning in both normal development and stress responses in plants. Here, we summarize the molecular mechanisms on the biosynthesis, metabolism, transport and signaling transduction pathways of CKs. CKs act as negative regulators of both root system architecture plasticity and root sodium exclusion in response to salt stress. The functions of CKs in mineral-toxicity tolerance and their detoxification in plants are reviewed. Comparative genomic analyses were performed to trace the origin, evolution and diversification of the critical regulatory networks linking CK signaling and abiotic stress. We found that the production of CKs and their derivatives, pathways of signal transduction and drought-response root growth regulation are evolutionarily conserved in land plants. In addition, the mechanisms of CK-mediated sodium exclusion under salt stress are suggested for further investigations. In summary, we propose that the manipulation of CK levels and their signaling pathways is important for plant abiotic stress and is, therefore, a potential strategy for meeting the increasing demand for global food production under changing climatic conditions.
Collapse
Affiliation(s)
- Lijun Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Qingfeng Zheng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Wei Jiang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Nayun Xiao
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Fanrong Zeng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Michelle Mak
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Fenglin Deng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| |
Collapse
|
12
|
Xu J, Yang C, Ji S, Ma H, Lin J, Li H, Chen S, Xu H, Zhong M. Heterologous expression of MirMAN enhances root development and salt tolerance in Arabidopsis. Front Plant Sci 2023; 14:1118548. [PMID: 37123825 PMCID: PMC10145921 DOI: 10.3389/fpls.2023.1118548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Introduction β-Mannanase is a plant cell wall remodeling enzyme involved in the breakdown of hemicellulose and plays an important role in growth by hydrolyzing the mannan-like polysaccharide, but its function in adaptation to salt stress has been less studied. Methods Based on cloned the mannanase (MAN) gene from Mirabilis jalapa L., the study was carried out by heterologously expressing the gene in Arabidopsis thaliana, and then observing the plant phenotypes and measuring relevant physiological and biochemical indicators under 150 mM salt treatment. Results and discussion The results indicate that MirMAN is a protein with a glycohydrolase-specific structural domain located in the cell wall. We first found that MirMAN reduced the susceptibility of transgenic Arabidopsis thaliana to high salt stress and increased the survival rate of plants by 38%. This was corroborated by the following significant changes, including the reduction in reactive oxygen species (ROS) levels, increase in antioxidant enzyme activity, accumulation of soluble sugars and increase of the expression level of RD29 in transgenic plants. We also found thatthe heterologous expression of MirMAN promoted root growth mainly by elongating the primary roots and increasing the density of lateral roots. Meanwhile, the expression of ARF7, ARF19, LBD16 and LBD29 was up-regulated in the transgenic plants, and the concentration of IAA in the roots was increased. Those results indicate that MirMAN is involved in the initiation of lateral root primordia in transgenic plants through the IAA-ARF signalling pathway. In conclusion, MirMAN improves plant salt tolerance not only by regulating ROS homeostasis, but also by promoting the development of lateral roots. Reflecting the potential of the MirMAN to promote root plastic development in adaptation to salt stress adversity.
Collapse
Affiliation(s)
- Juanjuan Xu
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Caiyu Yang
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Shangyao Ji
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hui Ma
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jingwei Lin
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hui Li
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Shuisen Chen
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hai Xu
- Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China
- *Correspondence: Ming Zhong, ; Hai Xu,
| | - Ming Zhong
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
- *Correspondence: Ming Zhong, ; Hai Xu,
| |
Collapse
|
13
|
Üstüner S, Schäfer P, Eichmann R. Development specifies, diversifies and empowers root immunity. EMBO Rep 2022; 23:e55631. [PMID: 36330761 PMCID: PMC9724680 DOI: 10.15252/embr.202255631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 08/04/2023] Open
Abstract
Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.
Collapse
Affiliation(s)
- Sim Üstüner
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| |
Collapse
|
14
|
Motte H, Fang T, Parizot B, Smet W, Yang X, Poelmans W, Walker L, Njo M, Bassel GW, Beeckman T. Cellular and gene expression patterns associated with root bifurcation in Selaginella. Plant Physiol 2022; 190:2398-2416. [PMID: 36029252 PMCID: PMC9706437 DOI: 10.1093/plphys/kiac402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The roots of lycophytes branch through dichotomy or bifurcation, during which the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, with LRs developing along the root axis at different distances from the apex. Although the process of root bifurcation is poorly understood, such knowledge can be important, because it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyte Selaginella moellendorffii. We characterized an in vitro developmental time frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching in S. moellendorffii at the microscopic and transcriptomic level. Our results showed that, in contrast to previous assumptions, initial cells (ICs) in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages of root branching argues for the occurrence of a symmetric division of the single IC, resulting in two apical stem cells that initiate root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome that resulted in the delineation of a subset of core meristem genes. The occurrence of multiple putative orthologs of meristem genes in this dataset suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance.
Collapse
Affiliation(s)
- Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wouter Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Xilan Yang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ward Poelmans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Liam Walker
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| |
Collapse
|
15
|
Mehra P, Pandey BK, Melebari D, Banda J, Leftley N, Couvreur V, Rowe J, Anfang M, De Gernier H, Morris E, Sturrock CJ, Mooney SJ, Swarup R, Faulkner C, Beeckman T, Bhalerao RP, Shani E, Jones AM, Dodd IC, Sharp RE, Sadanandom A, Draye X, Bennett MJ. Hydraulic flux-responsive hormone redistribution determines root branching. Science 2022; 378:762-768. [PMID: 36395221 DOI: 10.1126/science.add3771] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.
Collapse
Affiliation(s)
- Poonam Mehra
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Bipin K Pandey
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Dalia Melebari
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Jason Banda
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Nicola Leftley
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Valentin Couvreur
- Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - James Rowe
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Moran Anfang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Hugues De Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Center for Plant Systems Biology, VIB-UGent, 9052 Ghent, Belgium
| | - Emily Morris
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Craig J Sturrock
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Sacha J Mooney
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Ranjan Swarup
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | | | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Center for Plant Systems Biology, VIB-UGent, 9052 Ghent, Belgium
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Ian C Dodd
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Robert E Sharp
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Ari Sadanandom
- Department of Biosciences, University of Durham, Durham, UK
| | - Xavier Draye
- Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Malcolm J Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
16
|
Perez-Garcia P, Serrano-Ron L, Moreno-Risueno MA. The nature of the root clock at single cell resolution: Principles of communication and similarities with plant and animal pulsatile and circadian mechanisms. Curr Opin Cell Biol 2022; 77:102102. [DOI: 10.1016/j.ceb.2022.102102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/14/2022] [Accepted: 04/24/2022] [Indexed: 11/30/2022]
|
17
|
He W, Luo C, Wang Y, Wen X, Wang Y, Li T, Chen G, Zhao K, Li X, Fan C. Response Strategies of Root System Architecture to Soil Environment: A Case Study of Single-Species Cupressus funebris Plantations. Front Plant Sci 2022; 13:822223. [PMID: 35498661 PMCID: PMC9048025 DOI: 10.3389/fpls.2022.822223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The root system architecture (RSA), being a key characteristic of the root economic spectrum, describes the spatial arrangement and positioning of roots that determines the plant's exploration of water and nutrients in the soil. Still, it remains poorly understood how the RSA of woody plants responds to the demand for water and nutrients in different soil environments and how the uptake of these resources is optimized. Here we selected single-species plantations of Cupressus funebris and determined their topological index (TI), revised topological index (q a and q b ), root link length (RLL), root branching rate (R b and R i :R i+1), and in situ soil physicochemical properties to assess which root foraging strategies adopt in different soil environments among Guang'an City (GA), Suining City (SN), Mianyang City (MY), and Deyang City (DY) in China. We also tested the potential effects of different nutrients upon RSA according to its plastic phenotype. Principal component analysis (PCA) showed that levels of soil nutrients were the highest at DY, followed by MY and SN, and lower at GA. A dichotomous branching pattern was observed for GA, SN, and MY, but a herringbone branching pattern for DY. The RLL was ranked as GA, > SN, > MY > DY. The R b of GA, SN, and MY was significantly lower than that of DY (p < 0.05). Among the different city regions, values of R 1 /R 2 were the largest in different regions and those of R 4 /R 5 the smallest. The cross-sectional area of the root system did not differ between any two connected branch orders. The TI, q a , and RLL were significantly and negatively correlated with soil's water content, porosity, total nitrogen, total potassium, available nitrogen, and available phosphorus (p < 0.05), whereas they all had significant, positive relationships with soil temperature (p < 0.05). The R b was significantly and positively correlated with total potassium in soil (p < 0.05). Redundancy analysis showed that total potassium was the main factor driving variation in RSA. Our results emphasize that the RSA is capable of corresponding plastic alterations by changing its number of internal or external links and the root link length of fine roots vis-à-vis a heterogeneous environment, thereby optimizing the rates of water capture and space utilization.
Collapse
|
18
|
Cai B, Wang T, Sun H, Liu C, Chu J, Ren Z, Li Q. Gibberellins regulate lateral root development that is associated with auxin and cell wall metabolisms in cucumber. Plant Sci 2022; 317:110995. [PMID: 35193752 DOI: 10.1016/j.plantsci.2021.110995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 06/14/2023]
Abstract
Cucumber is an economically important crop cultivated worldwide. Gibberellins (GAs) play important roles in the development of lateral roots (LRs), which are critical for plant stress tolerance and productivity. Therefore, it is of great importance for cucumber production to study the role of GAs in LR development. Here, the results showed that GAs regulated cucumber LR development in a concentration-dependent manner. Treatment with 1, 10, 50 and 100 μM GA3 significantly increased secondary root length, tertiary root number and length. Of these, 50 μM GA3 treatment had strong effects on increasing root dry weight and the root/shoot dry weight ratio. Pairwise comparisons identified 417 down-regulated genes enriched for GA metabolism-related processes and 447 up-regulated genes enriched for cell wall metabolism-related processes in GA3-treated roots. A total of 3523 non-redundant DEGs were identified in our RNA-Seq data through pairwise comparisons and linear factorial modeling. Of these, most of the genes involved in auxin and cell wall metabolisms were up-regulated in GA3-treated roots. Our findings not only shed light on LR regulation mediated by GA but also offer an important resource for functional studies of candidate genes putatively involved in the regulation of LR development in cucumber and other crops.
Collapse
Affiliation(s)
- Bingbing Cai
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001, China.
| | - Ting Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Hong Sun
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Zhonghai Ren
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, Tai'an, Shandong, 271018, China.
| | - Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001, China.
| |
Collapse
|
19
|
Zhang Y, Umeda M, Kakimoto T. Pericycle cell division competence underlies various developmental programs. Plant Biotechnol (Tokyo) 2022; 39:29-36. [PMID: 35800961 PMCID: PMC9200087 DOI: 10.5511/plantbiotechnology.21.1202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2021] [Indexed: 05/08/2023]
Abstract
Pericycle cells possess proliferative activity long after leaving the root apical meristem. Depending on the developmental stage and external stimuli, pericycle cell division leads to the production of lateral roots, vascular cambium and periderm, and callus. Therefore, pericycle cell division competence underlies root branching and secondary growth, as well as plant regeneration capacity. In this review, we first briefly present an overview of the molecular pathways of the four developmental programs originated, exclusively or partly, from pericycle cells. Then, we provide a review of up-to-date knowledge in the mechanisms determining pericycle cells' competence to undergo cell division. Furthermore, we discuss directions of future research to further our understanding of the pericycle's characteristics and functions.
Collapse
Affiliation(s)
- Ye Zhang
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
- E-mail: Tel: +81-743-72-5592 Fax: +81-743-72-5599
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Tatsuo Kakimoto
- Department of Biology, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| |
Collapse
|
20
|
Richmond BL, Coelho CL, Wilkinson H, McKenna J, Ratchinski P, Schwarze M, Frost M, Lagunas B, Gifford ML. Elucidating connections between the strigolactone biosynthesis pathway, flavonoid production and root system architecture in Arabidopsis thaliana. Physiol Plant 2022; 174:e13681. [PMID: 35362177 PMCID: PMC9324854 DOI: 10.1111/ppl.13681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/01/2022] [Accepted: 03/29/2022] [Indexed: 05/20/2023]
Abstract
Strigolactones (SLs) are the most recently discovered phytohormones, and their roles in root architecture and metabolism are not fully understood. Here, we investigated four MORE AXILLARY GROWTH (MAX) SL mutants in Arabidopsis thaliana, max3-9, max4-1, max1-1 and max2-1, as well as the SL receptor mutant d14-1 and karrikin receptor mutant kai2-2. By characterising max2-1 and max4-1, we found that variation in SL biosynthesis modified multiple metabolic pathways in root tissue, including that of xyloglucan, triterpenoids, fatty acids and flavonoids. The transcription of key flavonoid biosynthetic genes, including TRANSPARENT TESTA4 (TT4) and TRANSPARENT TESTA5 (TT5) was downregulated in max2 roots and seedlings, indicating that the proposed MAX2 regulation of flavonoid biosynthesis has a widespread effect. We found an enrichment of BRI1-EMS-SUPPRESSOR 1 (BES1) targets amongst genes specifically altered in the max2 mutant, reflecting that the regulation of flavonoid biosynthesis likely occurs through the MAX2 degradation of BES1, a key brassinosteroid-related transcription factor. Finally, flavonoid accumulation decreased in max2-1 roots, supporting a role for MAX2 in regulating both SL and flavonoid biosynthesis.
Collapse
Affiliation(s)
| | | | | | | | | | - Maximillian Schwarze
- School of Life SciencesUniversity of WarwickCoventryUK
- School of BiosciencesBirminghamUK
| | - Matthew Frost
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | - Miriam L. Gifford
- School of Life SciencesUniversity of WarwickCoventryUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryUK
| |
Collapse
|
21
|
Xie X, Wang Y, Datla R, Ren M. Auxin and Target of Rapamycin Spatiotemporally Regulate Root Organogenesis. Int J Mol Sci 2021; 22:ijms222111357. [PMID: 34768785 PMCID: PMC8583787 DOI: 10.3390/ijms222111357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 12/17/2022] Open
Abstract
The programs associated with embryonic roots (ERs), primary roots (PRs), lateral roots (LRs), and adventitious roots (ARs) play crucial roles in the growth and development of roots in plants. The root functions are involved in diverse processes such as water and nutrient absorption and their utilization, the storage of photosynthetic products, and stress tolerance. Hormones and signaling pathways play regulatory roles during root development. Among these, auxin is the most important hormone regulating root development. The target of rapamycin (TOR) signaling pathway has also been shown to play a key role in root developmental programs. In this article, the milestones and influential progress of studying crosstalk between auxin and TOR during the development of ERs, PRs, LRs and ARs, as well as their functional implications in root morphogenesis, development, and architecture, are systematically summarized and discussed.
Collapse
Affiliation(s)
- Xiulan Xie
- Labarotary of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (X.X.); (Y.W.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Ying Wang
- Labarotary of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (X.X.); (Y.W.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Raju Datla
- Global Institute for Food Security in Saskatoon, University of Saskatchewan, Saskatoon, SK S7N 0W9, Canada
- Correspondence: (R.D.); (M.R.)
| | - Maozhi Ren
- Labarotary of Space Biology, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (X.X.); (Y.W.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou 450000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Correspondence: (R.D.); (M.R.)
| |
Collapse
|
22
|
Chen K, Zhang W, La T, Bastians PA, Guo T, Cao C. Microstructure investigation of plant architecture with X-ray microscopy. Plant Sci 2021; 311:110986. [PMID: 34482923 DOI: 10.1016/j.plantsci.2021.110986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
In recent years, the plant morphology has been well studied by multiple approaches at cellular and subcellular levels. Two-dimensional (2D) microscopy techniques offer imaging of plant structures on a wide range of magnifications for researchers. However, subcellular imaging is still challenging in plant tissues like roots and seeds. Here we use a three-dimensional (3D) imaging technology based on the X-ray microscope (XRM) and analyze several plant tissues from different plant species. The XRM provides new insights into plant structures using non-destructive imaging at high-resolution and high contrast. We also utilized a workflow aiming to acquire accurate and high-quality images in the context of the whole specimen. Multiple plant samples including rice, tobacco, Arabidopsis and maize were used to display the differences of phenotypes. Our work indicates that the XRM is a powerful tool to investigate plant microstructure in high-resolution scale. Our work also provides evidence that evaluate and quantify tissue specific differences for a range of plant species. We also characterize novel plant tissue phenotypes by the XRM, such as seeds in Arabidopsis, and utilize them for novel observation measurement. Our work represents an evaluated spatial and temporal resolution solution on seed observation and screening.
Collapse
Affiliation(s)
- Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, Guangdong, China; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), 23955-6900, Thuwal, Saudi Arabia
| | - Wenting Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ting La
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW, 2308, Australia
| | | | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academic of Sciences, Shanghai, 200032, China.
| | - Chunjie Cao
- Carl Zeiss (Shanghai) Co., Ltd, Beijing, 100191, China.
| |
Collapse
|
23
|
Fang T, Motte H, Parizot B, Beeckman T. Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants. Front Plant Sci 2021; 12:735514. [PMID: 34671375 PMCID: PMC8521068 DOI: 10.3389/fpls.2021.735514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.
Collapse
Affiliation(s)
- Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|
24
|
Primc A, Maizel A. Understanding lateral root formation, one cell at a time. Mol Plant 2021; 14:1229-1231. [PMID: 34216831 DOI: 10.1016/j.molp.2021.06.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 05/21/2023]
Affiliation(s)
- Anamarija Primc
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany.
| |
Collapse
|
25
|
Liang T, Yuan Z, Fu L, Zhu M, Luo X, Xu W, Yuan H, Zhu R, Hu Z, Wu X. Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice ( Oryza sativa L.). Int J Mol Sci 2021; 22:ijms22147674. [PMID: 34299294 PMCID: PMC8304609 DOI: 10.3390/ijms22147674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 01/21/2023] Open
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH4NO3 (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH4NO3 (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.
Collapse
Affiliation(s)
- Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhengqing Yuan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lu Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Menghan Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Luo
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xianting Wu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (T.L.); (Z.Y.); (L.F.); (M.Z.); (X.L.); (W.X.); (H.Y.); (R.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610000, China
- Correspondence: ; Tel.: +86-181-8061-4938
| |
Collapse
|
26
|
Vangheluwe N, Beeckman T. Lateral Root Initiation and the Analysis of Gene Function Using Genome Editing with CRISPR in Arabidopsis. Genes (Basel) 2021; 12:genes12060884. [PMID: 34201141 PMCID: PMC8227676 DOI: 10.3390/genes12060884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 11/24/2022] Open
Abstract
Lateral root initiation is a post-embryonic process that requires the specification of a subset of pericycle cells adjacent to the xylem pole in the primary root into lateral root founder cells. The first visible event of lateral root initiation in Arabidopsis is the simultaneous migration of nuclei in neighbouring founder cells. Coinciding cell cycle activation is essential for founder cells in the pericycle to undergo formative divisions, resulting in the development of a lateral root primordium (LRP). The plant signalling molecule, auxin, is a major regulator of lateral root development; the understanding of the molecular mechanisms controlling lateral root initiation has progressed tremendously by the use of the Arabidopsis model and a continual improvement of molecular methodologies. Here, we provide an overview of the visible events, cell cycle regulators, and auxin signalling cascades related to the initiation of a new LRP. Furthermore, we highlight the potential of genome editing technology to analyse gene function in lateral root initiation, which provides an excellent model to answer fundamental developmental questions such as coordinated cell division, growth axis establishment as well as the specification of cell fate and cell polarity.
Collapse
Affiliation(s)
- Nick Vangheluwe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Correspondence:
| |
Collapse
|
27
|
Zhang Y, Mitsuda N, Yoshizumi T, Horii Y, Oshima Y, Ohme-Takagi M, Matsui M, Kakimoto T. Two types of bHLH transcription factor determine the competence of the pericycle for lateral root initiation. Nat Plants 2021; 7:633-643. [PMID: 34007039 DOI: 10.1038/s41477-021-00919-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 04/15/2021] [Indexed: 05/26/2023]
Abstract
The molecular basis of the competence of the pericycle cell to initiate lateral root primordium formation is totally unknown. Here, we report that in Arabidopsis, two types of basic helix-loop-helix (bHLH) transcription factors, named PERICYCLE FACTOR TYPE-A (PFA) proteins and PERICYCLE FACTOR TYPE-B (PFB) proteins, govern the competence of pericycle cells to initiate lateral root primordium formation. Overexpression of PFA genes confers hallmark pericycle characteristics, including specific marker gene expression and auxin-induced cell division, and multiple loss-of-function mutations in PFA genes or the repression of PFB target genes results in the loss of this specific pericycle function. PFA and PFB proteins physically interact and are under mutual- and self-regulation, forming a positive feedback loop. This study unveils the transcriptional regulatory system that determines pericycle participation in lateral root initiation.
Collapse
Affiliation(s)
- Ye Zhang
- Department of Biology, Graduate School of Science, Osaka University, Osaka, Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Global Zero Emission Research Center, AIST, Tsukuba, Japan
| | - Takeshi Yoshizumi
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Takasaki University of Health and Welfare, Takasaki, Japan
| | - Yoko Horii
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yoshimi Oshima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Greenbio Research Center, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tatsuo Kakimoto
- Department of Biology, Graduate School of Science, Osaka University, Osaka, Japan.
| |
Collapse
|
28
|
Abstract
The root originated independently in euphyllophytes (ferns and seed plants) and lycophytes; however, the molecular evolutionary route of root initiation remains elusive. By analyses of the fern Ceratopteris richardii and seed plants, here we show that the molecular pathway involving auxin, intermediate-clade WUSCHEL-RELATED HOMEOBOX (IC-WOX) genes, and WUSCHEL-clade WOX (WC-WOX) genes could be conserved in root initiation. We propose that the "auxin>IC-WOX>WC-WOX" module in root initiation might have arisen in the common ancestor of euphyllophytes during the second origin of roots, and that this module has further developed during the evolution of different root types in ferns and seed plants.
Collapse
Affiliation(s)
- Jie Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Shaoting Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
29
|
Martinson WD, Byrne HM, Maini PK. Evaluating snail-trail frameworks for leader-follower behavior with agent-based modeling. Phys Rev E 2020; 102:062417. [PMID: 33466087 DOI: 10.1103/physreve.102.062417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Branched networks constitute a ubiquitous structure in biology, arising in plants, lungs, and the circulatory system; however, the mechanisms behind their creation are not well understood. A commonly used model for network morphogenesis proposes that sprouts develop through interactions between leader (tip) cells and follower (stalk) cells. In this description, tip cells emerge from existing structures, travel up chemoattractant gradients, and form new networks by guiding the movement of stalk cells. Such dynamics have been mathematically represented by continuum "snail-trail" models in which the tip cell flux contributes to the stalk cell proliferation rate. Although snail-trail models constitute a classical depiction of leader-follower behavior, their accuracy has yet to be evaluated in a rigorous quantitative setting. Here, we extend the snail-trail modeling framework to two spatial dimensions by introducing a novel multiplicative factor to the stalk cell rate equation, which corrects for neglected network creation in directions other than that of the migrating front. Our derivation of this factor demonstrates that snail-trail models are valid descriptions of cell dynamics when chemotaxis dominates cell movement. We confirm that our snail-trail model accurately predicts the dynamics of tip and stalk cells in an existing agent-based model (ABM) for network formation [Pillay et al., Phys. Rev. E 95, 012410 (2017)10.1103/PhysRevE.95.012410]. We also derive conditions for which it is appropriate to use a reduced, one-dimensional snail-trail model to analyze ABM results. Our analysis identifies key metrics for cell migration that may be used to anticipate when simple snail-trail models will accurately describe experimentally observed cell dynamics in network formation.
Collapse
Affiliation(s)
- W Duncan Martinson
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, United Kingdom
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, United Kingdom
| | - Philip K Maini
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, United Kingdom
| |
Collapse
|
30
|
Baesso B, Terzaghi M, Chiatante D, Scippa GS, Montagnoli A. WOX genes expression during the formation of new lateral roots from secondary structures in Populus nigra (L.) taproot. Sci Rep 2020; 10:18890. [PMID: 33144589 PMCID: PMC7641218 DOI: 10.1038/s41598-020-75150-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 10/08/2020] [Indexed: 11/28/2022] Open
Abstract
Despite the large amounts of data available on lateral root formation, little is known about their initiation from secondary structures. In the present work, we applied a bending treatment to Populus nigra (L.) woody taproots to induce the formation of new lateral roots. The development of lateral roots was monitored by stereomicroscopic examination of cross-sections. Tissues were sampled from the bending zone in the proximity of the vascular cambium before (time 0) and after the application of bending at three different time points (24, 48, and 72 h) and analyzed for the expression of P. nigra WOX homologs. The initiation of new lateral roots was observed to originate from the vascular cambium zone and was followed by primordium formation and root emergence. PnWOX4a, PnWOX4b, PnWOX5a, PnWOX5b, PnWOX11/12a, and PnWOX11/12b were shown to be expressed during the formation of new lateral roots at different developmental stages. The mechanical stress simulated by bending treatment was shown to activate the molecular mechanism leading to the expression of WOX genes, which are hypothesized to control SLR formation in the cambium zone of poplar taproot.
Collapse
Affiliation(s)
- Barbara Baesso
- Department of Biotechnology and Life Science, University of Insubria, Via Dunant, 3, 21100, Varese, VA, Italy
| | - Mattia Terzaghi
- Department of Chemistry and Biology 'A. Zambelli', University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Donato Chiatante
- Department of Biotechnology and Life Science, University of Insubria, Via Dunant, 3, 21100, Varese, VA, Italy
| | - Gabriella Stefania Scippa
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090, Pesche, IS, Italy
| | - Antonio Montagnoli
- Department of Biotechnology and Life Science, University of Insubria, Via Dunant, 3, 21100, Varese, VA, Italy.
| |
Collapse
|
31
|
Liu B, Wu J, Yang S, Schiefelbein J, Gan Y. Nitrate regulation of lateral root and root hair development in plants. J Exp Bot 2020; 71:4405-4414. [PMID: 31796961 PMCID: PMC7382377 DOI: 10.1093/jxb/erz536] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/03/2019] [Indexed: 05/16/2023]
Abstract
Nitrogen (N) is one of the most important macronutrients for plant growth and development. However, the concentration and distribution of N varies in soil due to a variety of environmental factors. In response, higher plants have evolved a developmentally flexible root system to efficiently take up N under N-limited conditions. Over the past decade, significant progress has been made in understanding this form of plant 'root-foraging' behavior, which is controlled by both a local and a long-distance systemic nitrate signaling pathway. In this review, we focus on the key components of nitrate perception, signaling, and transduction and its role in lateral root development. We also highlight recent findings on the molecular mechanisms of the nitrate systemic signaling pathway, including small signaling peptides involved in long-distance shoot-root communication. Furthermore, we summarize the transcription factor networks responsible for nitrate-dependent lateral root and root hair development.
Collapse
Affiliation(s)
- Bohan Liu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Junyu Wu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuaiqi Yang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Correspondence: or
| | - Yinbo Gan
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Correspondence: or
| |
Collapse
|
32
|
Champreux A, Meyer-Berthaud B, Decombeix AL. Keraphyton gen. nov., a new Late Devonian fern-like plant from Australia. PeerJ 2020; 8:e9321. [PMID: 32587800 PMCID: PMC7304422 DOI: 10.7717/peerj.9321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/18/2020] [Indexed: 12/02/2022] Open
Abstract
The first plants related to the ferns are represented by several extinct groups that emerged during the Devonian. Among them, the iridopterids are closely allied to the sphenopsids, a group represented today by the genus Equisetum. They have been documented in Middle to early Late Devonian deposits of Laurussia and the Kazakhstan plate. Their Gondwanan record is poor, with occurrences limited to Venezuela and Morocco. Here we describe a new genus from a late Late Devonian locality of New South Wales. It is represented by a single anatomically preserved large stem characterized by a star-shaped vascular system with protoxylem strands located at rib tips, and by a lack of secondary tissues. Within the first fern-like plants, this stem shares the largest number of characters with iridopterid axes but differs by the pattern of its vascular system. Keraphyton mawsoniae gen. et sp. nov. adds a new record of early fern-like plants in eastern Gondwana. It provides new insights into the anatomical diversity within this key group of plants and supports the distinctiveness of the Australian flora in the latest Devonian.
Collapse
Affiliation(s)
- Antoine Champreux
- AMAP, Université de Montpellier, CIRAD, CNRS, INRA, IRD, Montpellier, France.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | | |
Collapse
|
33
|
Velinov V, Vaseva I, Zehirov G, Zhiponova M, Georgieva M, Vangheluwe N, Beeckman T, Vassileva V. Overexpression of the NMig1 Gene Encoding a NudC Domain Protein Enhances Root Growth and Abiotic Stress Tolerance in Arabidopsis thaliana. Front Plant Sci 2020; 11:815. [PMID: 32595686 PMCID: PMC7301909 DOI: 10.3389/fpls.2020.00815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/20/2020] [Indexed: 05/31/2023]
Abstract
The family of NudC proteins has representatives in all eukaryotes and plays essential evolutionarily conserved roles in many aspects of organismal development and stress response, including nuclear migration, cell division, folding and stabilization of other proteins. This study investigates an undescribed Arabidopsis homolog of the Aspergillus nidulans NudC gene, named NMig1 (for Nuclear Migration 1), which shares high sequence similarity to other plant and mammalian NudC-like genes. Expression of NMig1 was highly upregulated in response to several abiotic stress factors, such as heat shock, drought and high salinity. Constitutive overexpression of NMig1 led to enhanced root growth and lateral root development under optimal and stress conditions. Exposure to abiotic stress resulted in relatively weaker inhibition of root length and branching in NMig1-overexpressing plants, compared to the wild-type Col-0. The expression level of antioxidant enzyme-encoding genes and other stress-associated genes was considerably induced in the transgenic plants. The increased expression of the major antioxidant enzymes and greater antioxidant potential correlated well with the lower levels of reactive oxygen species (ROS) and lower lipid peroxidation. In addition, the overexpression of NMig1 was associated with strong upregulation of genes encoding heat shock proteins and abiotic stress-associated genes. Therefore, our data demonstrate that the NudC homolog NMig1 could be considered as a potentially important target gene for further use, including breeding more resilient crops with improved root architecture under abiotic stress.
Collapse
Affiliation(s)
- Valentin Velinov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irina Vaseva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Grigor Zehirov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Mariana Georgieva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nick Vangheluwe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| |
Collapse
|
34
|
Perotti MF, Ariel FD, Chan RL. Lateral root development differs between main and secondary roots and depends on the ecotype. Plant Signal Behav 2020; 15:1755504. [PMID: 32310024 PMCID: PMC8570754 DOI: 10.1080/15592324.2020.1755504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Root architecture depends on the development of the main root and also on the number and density of lateral roots. Most molecular knowledge about the development of lateral roots was acquired studying primary roots, and it was implied that high order roots follow the same pattern. Recently, we informed that AtHB23 is differentially regulated in primary and secondary roots. Here we show that LBD16, a target of AtHB23, also is differentially regulated; it is expressed in the tip of secondary and tertiary roots but not in primary ones. Moreover, the key hormone auxin exhibits a different distribution pattern in secondary and tertiary roots, according to the reporter DR5. Finally, we show that in Col 0 and Ler ecotypes development of secondary and tertiary roots exhibits significant variations. Altogether, we can conclude that different genetic programs govern secondary and tertiary roots development and such processes are dependent on the Arabidopsis genotype.
Collapse
Affiliation(s)
- María Florencia Perotti
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| | - Federico Damián Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| | - Raquel Lía Chan
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| |
Collapse
|
35
|
Hetherington AJ, Berry CM, Dolan L. Multiple origins of dichotomous and lateral branching during root evolution. Nat Plants 2020; 6:454-459. [PMID: 32366983 DOI: 10.1038/s41477-020-0646-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Roots of extant vascular plants proliferate through lateral branching (euphyllophytes) or dichotomy (lycophytes)1-4. The origin of these distinct modes of branching was key for plant evolution because they enabled the development of structurally and functionally different root systems that supported a diversity of shoot systems3-6. It has been unclear when lateral branching originated and how many times it evolved4,7,8. Here, we report that many euphyllophytes that were extant during the Devonian and Carboniferous periods developed dichotomous roots. Our data indicate that dichotomous root branching evolved in both lycophytes and euphyllophytes. Lateral roots then evolved at different times in three major lineages of extant euphyllophytes-the lignophytes, ferns and horsetails. The multiple origins of dichotomous and lateral root branching are extreme cases of convergent evolution that occurred during the Devonian and Carboniferous periods when the land-plant flora underwent a radiation in morphological diversity.
Collapse
Affiliation(s)
| | | | - Liam Dolan
- Department of Plant Sciences, University of Oxford, Oxford, UK
| |
Collapse
|
36
|
De-Jesús-García R, Rosas U, Dubrovsky JG. The barrier function of plant roots: biological bases for selective uptake and avoidance of soil compounds. Funct Plant Biol 2020; 47:383-397. [PMID: 32213271 DOI: 10.1071/fp19144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
The root is the main organ through which water and mineral nutrients enter the plant organism. In addition, root fulfils several other functions. Here, we propose that the root also performs the barrier function, which is essential not only for plant survival but for plant acclimation and adaptation to a constantly changing and heterogeneous soil environment. This function is related to selective uptake and avoidance of some soil compounds at the whole plant level. We review the toolkit of morpho-anatomical, structural, and other components that support this view. The components of the root structure involved in selectivity, permeability or barrier at a cellular, tissue, and organ level and their properties are discussed. In consideration of the arguments supporting barrier function of plant roots, evolutionary aspects of this function are also reviewed. Additionally, natural variation in selective root permeability is discussed which suggests that the barrier function is constantly evolving and is subject of natural selection.
Collapse
Affiliation(s)
- Ramces De-Jesús-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenuenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenuenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; and Corresponding author.
| |
Collapse
|
37
|
Arsova B, Foster KJ, Shelden MC, Bramley H, Watt M. Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake. New Phytol 2020; 225:1111-1119. [PMID: 31127613 DOI: 10.1111/nph.15955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/19/2019] [Indexed: 05/12/2023]
Abstract
Plants are inherently dynamic. Dynamics minimize stress while enabling plants to flexibly acquire resources. Three examples are presented for plants tolerating saline soil: transport of sodium chloride (NaCl), water and macronutrients is nonuniform along a branched root; water and NaCl redistribute between shoot and soil at night-time; and ATP for salt exclusion is much lower in thinner branch roots than main roots, quantified using a biophysical model and geometry from anatomy. Noninvasive phenotyping and precision agriculture technologies can be used together to harness plant dynamics, but analytical methods are needed. A plant advancing in time through a soil and atmosphere space is proposed as a framework for dynamic data and their relationship to crop improvement.
Collapse
Affiliation(s)
- Borjana Arsova
- Root Dynamics Group, Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, 52428, Germany
| | - Kylie J Foster
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Megan C Shelden
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
| | - Michelle Watt
- Root Dynamics Group, Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, 52428, Germany
| |
Collapse
|
38
|
Motte H, Parizot B, Fang T, Beeckman T. The evolutionary trajectory of root stem cells. Curr Opin Plant Biol 2020; 53:23-30. [PMID: 31707318 DOI: 10.1016/j.pbi.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/05/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Root stem cells are crucial for the establishment of roots and are therefore a major evolutionary innovation that enabled land plants to spread on land. Despite their importance, not too much is known about the origin and the molecular players installing and maintaining them. Although still fragmentary, the recent availability of new data for early land plants can be used to identify and analyze the conservation of key regulators of root meristems. In this review, we evaluate the possible conservation of important root stem cell regulators to suggest pathways that might have been important at the origin of roots.
Collapse
Affiliation(s)
- Hans Motte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Boris Parizot
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tao Fang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| |
Collapse
|
39
|
Nelissen H, Gonzalez N. Understanding plant organ growth: a multidisciplinary field. J Exp Bot 2020; 71:7-10. [PMID: 31725876 DOI: 10.1093/jxb/erz448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium
| | - Nathalie Gonzalez
- INRA, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882, Villenave d'Ornon cedex, France
| |
Collapse
|
40
|
Perotti MF, Ribone PA, Cabello JV, Ariel FD, Chan RL. AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots. Plant J 2019; 100:1224-1236. [PMID: 31444832 DOI: 10.1111/tpj.14511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/02/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.
Collapse
Affiliation(s)
- María F Perotti
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Pamela A Ribone
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Julieta V Cabello
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| |
Collapse
|
41
|
Ljubotina MK, Cahill JF. Effects of neighbour location and nutrient distributions on root foraging behaviour of the common sunflower. Proc Biol Sci 2019; 286:20190955. [PMID: 31530149 PMCID: PMC6784730 DOI: 10.1098/rspb.2019.0955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/28/2019] [Indexed: 01/05/2023] Open
Abstract
Plants regularly encounter patchily distributed soil nutrients. A common foraging response is to proliferate roots within high-quality patches. The influence of the social environment on this behaviour has been given limited attention, despite important fitness consequences of competition for soil resources among plants. Using the common sunflower (Helianthus annuus L.), we compared localized root proliferation in a high-quality patch by plants grown alone to that of plants in two different social environments: with a neighbouring plant sharing equal access to the high-quality patch, and with a neighbouring plant present but farther from the high-quality patch such that the focal individual was in closer proximity to the high-quality patch. Sunflowers grown alone proliferated more roots within high-nutrient patches than lower-nutrient soil. Plants decreased root proliferation within a high-nutrient patch when it was equidistant to a neighbour. Conversely, plants increased root proliferation when they were in closer proximity to the patch relative to a nearby neighbour. Such contingent responses may allow sunflowers to avoid competition in highly contested patches, but to also pre-empt soil resources from neighbours when they have better access to a high-quality patch. We also compared patch occupancy by sunflowers grown alone with two equidistant high-quality patches to occupancy by sunflowers grown with two high-quality patches and a neighbour. Plants grown with a neighbour decreased root length within shared patches but did not increase root length within high-quality patches they were in closer proximity to, perhaps because resource pre-emption may be less important for individuals when resources are more abundant. These results show that nutrient foraging responses in plants can be socially contingent, and that plants may account for the possibility of pre-empting limited resources in their foraging decisions.
Collapse
Affiliation(s)
- Megan K. Ljubotina
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, CanadaT6G 2E9
| | | |
Collapse
|
42
|
Abstract
In order to optimally establish their root systems, plants are endowed with several mechanisms to use at distinct steps during their development. In this review, we zoom in on the major processes involved in root development and detail important new insights that have been generated in recent studies, mainly using the Arabidopsis root as a model. First, we discuss new insights in primary root development with the characterization of tissue-specific transcription factor complexes and the identification of non-cell-autonomous control mechanisms in the root apical meristem. Next, root branching is discussed by focusing on the earliest steps in the development of a new lateral root and control of its postemergence growth. Finally, we discuss the impact of phosphate, nitrogen, and water availability on root development and summarize current knowledge about the major molecular mechanisms involved.
Collapse
Affiliation(s)
- Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium;
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium;
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon 21985, Republic of Korea
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium;
| |
Collapse
|
43
|
Kiryushkin AS, Ilina EL, Puchkova VA, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in the Parental Root Meristem of Cucurbits: Old Players in a New Position. Front Plant Sci 2019; 10:365. [PMID: 31110507 PMCID: PMC6499211 DOI: 10.3389/fpls.2019.00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/08/2019] [Indexed: 05/12/2023]
Abstract
While in most higher plants, including the model system Arabidopsis thaliana, the formation of lateral root primordia is induced in the elongation zone of the parental root, in seven plant families, including Cucurbitaceae, an alternative root branching mechanism is established such that lateral roots are initiated directly in the apical meristem of the parental root. In Arabidopsis, the transcription factor GATA23 and MEMBRANE-ASSOCIATED KINASE REGULATOR4 (MAKR4) are involved in the gene regulatory network of lateral root initiation. Among all marker genes examined, these are the earliest known marker genes up-regulated by auxin during lateral root initiation. In this study, putative functional orthologs of Arabidopsis GATA23 and MAKR4 were identified in cucumber (Cucumis sativus) and squash (Cucurbita pepo). Both cucurbits contained 26 genes encoding GATA family transcription factors and only one MAKR4 gene. Phylogenetic and transcriptional analysis of up-regulation by auxin led to the identification of GATA23 putative functional orthologs in Cucurbitaceae - CpGATA24 and CsGATA24. In squash, CpMAKR4 was up-regulated by naphthylacetic acid (NAA) and, similar to MAKR4 in Arabidopsis, indole-3-butyric acid (IBA). A detailed analysis of the expression pattern of CpGATA24 and CpMAKR4 in squash roots from founder cell specification until emergence of lateral root primordia was carried out using promoter-fluorescent reporter gene fusions and confocal microscopy. Their expression was induced in the protoxylem, and then expanded to founder cells in the pericycle. Thus, while the overall expression pattern of these genes was significantly different from that in Arabidopsis, in founder cells their expression was induced in the same order as in Arabidopsis. Altogether, these findings suggest that in Cucurbitaceae the putative functional orthologs of GATA23 and MAKR4 might play a role in founder cell specification and primordium positioning during lateral root initiation. The role of the protoxylem in auxin transport as a trigger of founder cells specification and lateral root initiation is discussed.
Collapse
Affiliation(s)
- Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Elena L. Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vera A. Puchkova
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Elizaveta D. Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| |
Collapse
|
44
|
Fang T, Motte H, Parizot B, Beeckman T. Root Branching Is Not Induced by Auxins in Selaginella moellendorffii. Front Plant Sci 2019; 10:154. [PMID: 30842783 PMCID: PMC6391681 DOI: 10.3389/fpls.2019.00154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Angiosperms develop intensively branched root systems that are accommodated with the high capacity to produce plenty of new lateral roots throughout their life-span. Root branching can be dynamically regulated in response to edaphic conditions and provides the plants with a soil-mining potential. This highly specialized branching capacity has most likely been key in the colonization success of the present flowering plants on our planet. The initiation, formation and outgrowth of branching roots in Angiosperms are dominated by the plant hormone auxin. Upon auxin treatment root branching through the formation of lateral roots can easily be induced. In this study, we questioned whether this strong branching-inducing action of auxin is part of a conserved mechanism that was already active in the earliest diverging lineage of vascular plants with roots. In Selaginella, an extant representative species of this early clade of root forming plants, components of the canonical auxin signaling pathway are retrieved in its genome. Although we observed a clear physiological response and an indirect effect on root branching, we were not able to directly induce root branching in this species by application of different auxins. We conclude that the structural and developmental difference of the Selaginella root, which branches via bifurcation of the root meristem, or the absence of an auxin-mediated root development program, is most likely causative for the absence of an auxin-induced branching mechanism.
Collapse
Affiliation(s)
- Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|