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Jan M, Muhammad S, Jin W, Zhong W, Zhang S, Lin Y, Zhou Y, Liu J, Liu H, Munir R, Yue Q, Afzal M, Wang G. Modulating root system architecture: cross-talk between auxin and phytohormones. FRONTIERS IN PLANT SCIENCE 2024; 15:1343928. [PMID: 38390293 PMCID: PMC10881875 DOI: 10.3389/fpls.2024.1343928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/08/2024] [Indexed: 02/24/2024]
Abstract
Root architecture is an important agronomic trait that plays an essential role in water uptake, soil compactions, nutrient recycling, plant-microbe interactions, and hormone-mediated signaling pathways. Recently, significant advancements have been made in understanding how the complex interactions of phytohormones regulate the dynamic organization of root architecture in crops. Moreover, phytohormones, particularly auxin, act as internal regulators of root development in soil, starting from the early organogenesis to the formation of root hair (RH) through diverse signaling mechanisms. However, a considerable gap remains in understanding the hormonal cross-talk during various developmental stages of roots. This review examines the dynamic aspects of phytohormone signaling, cross-talk mechanisms, and the activation of transcription factors (TFs) throughout various developmental stages of the root life cycle. Understanding these developmental processes, together with hormonal signaling and molecular engineering in crops, can improve our knowledge of root development under various environmental conditions.
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Affiliation(s)
- Mehmood Jan
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Sajid Muhammad
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Weicai Jin
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- Heyuan Division of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, Guangdong, China
| | - Wenhao Zhong
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shaolong Zhang
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- Heyuan Division of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, Guangdong, China
| | - Yanjie Lin
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yueni Zhou
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jinlong Liu
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Haifeng Liu
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- Heyuan Division of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, Guangdong, China
| | - Raheel Munir
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qiang Yue
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
| | - Muhammad Afzal
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- Heyuan Division of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, Guangdong, China
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2
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Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). THE PLANT CELL 2022; 34:4816-4839. [PMID: 36040191 PMCID: PMC9709996 DOI: 10.1093/plcell/koac270] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/25/2022] [Indexed: 05/21/2023]
Abstract
Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of VLCFAs and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level.
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Affiliation(s)
| | | | - Liping Zhu
- College of Life Sciences, Shaanxi Normal University, Xi’an,
China
| | - Bin Jiang
- College of Life Sciences, Shaanxi Normal University, Xi’an,
China
| | - Huiqin Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an,
China
| | - Ruxi Gao
- College of Life Sciences, Northwest A&F University,
Shaanxi, Yangling, China
| | - Jiří Friml
- Institute of Science and Technology Austria, 3400
Klosterneuburg, Austria
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Song JH, Montes-Luz B, Tadra-Sfeir MZ, Cui Y, Su L, Xu D, Stacey G. High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation. FRONTIERS IN PLANT SCIENCE 2022; 13:820348. [PMID: 35498680 PMCID: PMC9048599 DOI: 10.3389/fpls.2022.820348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Nodule organogenesis in legumes is regulated temporally and spatially through gene networks. Genome-wide transcriptome, proteomic, and metabolomic analyses have been used previously to define the functional role of various plant genes in the nodulation process. However, while significant progress has been made, most of these studies have suffered from tissue dilution since only a few cells/root regions respond to rhizobial infection, with much of the root non-responsive. To partially overcome this issue, we adopted translating ribosome affinity purification (TRAP) to specifically monitor the response of the root cortex to rhizobial inoculation using a cortex-specific promoter. While previous studies have largely focused on the plant response within the root epidermis (e.g., root hairs) or within developing nodules, much less is known about the early responses within the root cortex, such as in relation to the development of the nodule primordium or growth of the infection thread. We focused on identifying genes specifically regulated during early nodule organogenesis using roots inoculated with Bradyrhizobium japonicum. A number of novel nodulation gene candidates were discovered, as well as soybean orthologs of nodulation genes previously reported in other legumes. The differential cortex expression of several genes was confirmed using a promoter-GUS analysis, and RNAi was used to investigate gene function. Notably, a number of differentially regulated genes involved in phytohormone signaling, including auxin, cytokinin, and gibberellic acid (GA), were also discovered, providing deep insight into phytohormone signaling during early nodule development.
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Affiliation(s)
- Jae Hyo Song
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Bruna Montes-Luz
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Michelle Zibetti Tadra-Sfeir
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Yaya Cui
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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4
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Bobrovskikh A, Doroshkov A, Mazzoleni S, Cartenì F, Giannino F, Zubairova U. A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis. Front Genet 2021; 12:652974. [PMID: 34093652 PMCID: PMC8176226 DOI: 10.3389/fgene.2021.652974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants' features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem's solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells' spatial localization in the initial plant organ-one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.
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Affiliation(s)
- Aleksandr Bobrovskikh
- Laboratory of Plant Growth Biomechanics, Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.,Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Alexey Doroshkov
- Laboratory of Plant Growth Biomechanics, Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Fabrizio Cartenì
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Francesco Giannino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Ulyana Zubairova
- Laboratory of Plant Growth Biomechanics, Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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5
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Coate JE, Farmer AD, Schiefelbein JW, Doyle JJ. Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots. Front Genet 2020; 11:596150. [PMID: 33240334 PMCID: PMC7670048 DOI: 10.3389/fgene.2020.596150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/12/2020] [Indexed: 01/11/2023] Open
Abstract
Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralog pairs rapidly return to single copy status whereas, in other pairs, both paralogs are retained and may diverge in expression pattern or function. The effect of a gene - its site of expression and thus the initial locus of its function - occurs at the level of a cell comprising a single cell type at a given state of the cell's development. Using Arabidopsis thaliana single cell transcriptomic data we categorized patterns of expression for 11,470 duplicate gene pairs across 36 cell clusters comprising nine cell types and their developmental states. Among these 11,470 pairs, 10,187 (88.8%) had at least one copy expressed in at least one of the 36 cell clusters. Pairs produced by WGD more often had both paralogs expressed in root cells than did pairs produced by small scale duplications. Three quarters of gene pairs expressed in the 36 cell clusters (7,608/10,187) showed extreme expression bias in at least one cluster, including 352 cases of reciprocal bias, a pattern consistent with expression subfunctionalization. More than twice as many pairs showed reciprocal expression bias between cell states than between cell types or between roots and leaves. A group of 33 gene pairs with reciprocal expression bias showed evidence of concerted divergence of gene networks in stele vs. epidermis. Pairs with both paralogs expressed without bias were less likely to have paralogs with divergent mutant phenotypes; such bias-free pairs showed evidence of preservation by maintenance of dosage balance. Overall, we found considerable evidence of shifts in gene expression following duplication, including in >80% of pairs encoding 7,653 genes expressed ubiquitously in all root cell types and states for which we inferred the polarity of change.
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Affiliation(s)
- Jeremy E. Coate
- Department of Biology, Reed College, Portland, OR, United States
| | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, NM, United States
| | - John W. Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Jeff J. Doyle
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, United States
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Hoang NT, Tóth K, Stacey G. The role of microRNAs in the legume-Rhizobium nitrogen-fixing symbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1668-1680. [PMID: 32163588 DOI: 10.1093/jxb/eraa018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20-24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.
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Affiliation(s)
- Nhung T Hoang
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| | - Katalin Tóth
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| | - Gary Stacey
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
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7
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Abstract
Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules, mature nodules, emerging lateral roots and young lateral roots, and constructed strand-specific RNA sequencing (RNAseq) libraries using polyA-enriched RNA preparations. Root sections above and below these organs, devoid of any lateral organs, were used to construct respective control tissue libraries. High sequence quality, predominant mapping to coding sequences, and consistency between replicates indicated that the RNAseq libraries were of a very high quality. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. Potential uses for this high quality transcriptome data set include generation of global gene regulatory networks to identify key regulators; metabolic pathway analyses and comparative analyses of key gene families to discover organ-specific biological processes; and identification of organ-specific alternate spliced transcripts. When combined with other similar datasets, especially from leguminous plants, these analyses can help answer questions on the evolutionary origins of root nodules and relationships between the development of different plant lateral organs.
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8
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Yuan Y, Lee H, Hu H, Scheben A, Edwards D. Single-Cell Genomic Analysis in Plants. Genes (Basel) 2018; 9:genes9010050. [PMID: 29361790 PMCID: PMC5793201 DOI: 10.3390/genes9010050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 12/26/2022] Open
Abstract
Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.
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Affiliation(s)
- Yuxuan Yuan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - HueyTyng Lee
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
- School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
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9
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Qiao Z, Pingault L, Zogli P, Langevin M, Rech N, Farmer A, Libault M. A comparative genomic and transcriptomic analysis at the level of isolated root hair cells reveals new conserved root hair regulatory elements. PLANT MOLECULAR BIOLOGY 2017; 94:641-655. [PMID: 28687904 DOI: 10.1007/s11103-017-0630-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication. Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited by the quality of the genomic and transcriptomic resources available. Specifically, the transcriptomes generated from plant organs are the reflection of the contribution of the different cell types composing the samples weighted by their relative abundances in the sample. These contributions can vary between plant species leading to the generation of datasets which are difficult to compare. To gain a deeper understanding of the evolution of gene transcription in and between plant species, we performed a comparative transcriptomic and genomic analysis at the level of one single plant cell type, the root hair cell, and between two model plants: Arabidopsis (Arabidopsis thaliana) and soybean (Glycine max). These two species, which diverged 90 million years ago, were selected as models based on the large amount of genomic and root hair transcriptomic information currently available. Our analysis revealed in detail the transcriptional divergence and conservation between soybean paralogs (i.e., the soybean genome is the product of two successive whole genome duplications) and between Arabidopsis and soybean orthologs in this single plant cell type. Taking advantage of this evolutionary study, we combined bioinformatics, molecular, cellular and microscopic tools to characterize plant promoter sequences and the discovery of two root hair regulatory elements (RHE1 and RHE2) consistently and specifically active in plant root hair cells.
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Affiliation(s)
- Zhenzhen Qiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Lise Pingault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Micaela Langevin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Niccole Rech
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
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10
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Hey S, Baldauf J, Opitz N, Lithio A, Pasha A, Provart N, Nettleton D, Hochholdinger F. Complexity and specificity of the maize (Zea mays L.) root hair transcriptome. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2175-2185. [PMID: 28398587 PMCID: PMC5447894 DOI: 10.1093/jxb/erx104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and their phylogenetic relationship and expression in root hairs were determined. This study indicated that the genetic regulation of root hair development in Arabidopsis and maize is controlled by common genes, but also shows differences which need to be dissected in future genetic experiments. Finally, a maize root view of the eFP browser was implemented including the root hair transcriptome of the present study and several previously published maize root transcriptome data sets. The eFP browser provides color-coded expression levels for these root types and tissues for any gene of interest, thus providing a novel resource to study gene expression and function in maize roots.
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Affiliation(s)
- Stefan Hey
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Jutta Baldauf
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Nina Opitz
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
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11
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Hossain MS, Kawakatsu T, Kim KD, Zhang N, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. THE NEW PHYTOLOGIST 2017; 214:808-819. [PMID: 28106918 DOI: 10.1111/nph.14421] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/01/2016] [Indexed: 05/23/2023]
Abstract
Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated than were stripped roots. However, in response to heat stress, both root hairs and stripped roots showed hypomethylation in each context, especially in the CHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes in DNA methylation are directly or indirectly associated with expression of genes and transposons within the context of either specific tissues/cells or stress (heat).
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Affiliation(s)
- Md Shakhawat Hossain
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Taiji Kawakatsu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 30508602, Japan
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Ning Zhang
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Cuong T Nguyen
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Saad M Khan
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Josef M Batek
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Robert J Schmitz
- Department of Genetics, The University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Dong Xu
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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12
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Wei F, Fanella B, Guo L, Wang X. Membrane glycerolipidome of soybean root hairs and its response to nitrogen and phosphate availability. Sci Rep 2016; 6:36172. [PMID: 27812010 PMCID: PMC5095881 DOI: 10.1038/srep36172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/07/2016] [Indexed: 11/10/2022] Open
Abstract
Root hairs are tubular extensions of specific root epidermal cells important in plant nutrition and water absorption. To determine membrane glycerolipids in root hairs and roots may differ, as well as their respective response to nutrient availability, this study analyzed the membrane glycerolipid species in soybean root hairs and in roots stripped of root hairs, and their response to nitrogen (N) and phosphate (Pi) supplementation. The ratio of phospholipids to galactolipids was 1.5 fold higher in root hairs than in stripped roots. Under Pi deficiency, the ratio of phospholipids to galactolipids in stripped roots decreased with the greatest decrease found in the level of phosphatidylethanolamine (PE) in root hairs and stripped roots, and root hairs had an increased level of phosphatidic acid (PA). When seedlings were not supplied with N, the level of the N-containing lipids PE and phosphatidylserine in root hairs decreased whereas the level of non-N-containing lipids galactolipids and PA increased compared to N-supplied conditions. In stripped roots, the level of major membrane lipids was not different between N-sufficient and -deficient conditions. The results indicate that the membrane glycerolipidomes in root hairs are more responsive to nutrient availability than are the rest of roots.
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Affiliation(s)
- Fang Wei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, Wuhan, Hubei, 430062, China
| | - Brian Fanella
- Department of Biology, University of Missouri, St. Louis, MO 63121, USA
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO 63121, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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13
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Doyle JJ. Chasing unicorns: Nodulation origins and the paradox of novelty. AMERICAN JOURNAL OF BOTANY 2016; 103:1865-1868. [PMID: 27756731 DOI: 10.3732/ajb.1600260] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/31/2016] [Indexed: 05/25/2023]
Affiliation(s)
- Jeff J Doyle
- School of Integrative Plant Science, Section of Plant Breeding & Genetics and Section of Plant Biology, 240 Emerson Hall, Cornell University, Ithaca, New York 14853 USA
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14
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Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4182071. [PMID: 27088086 PMCID: PMC4818802 DOI: 10.1155/2016/4182071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/18/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
Abstract
The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.
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15
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Damiani I, Drain A, Guichard M, Balzergue S, Boscari A, Boyer JC, Brunaud V, Cottaz S, Rancurel C, Da Rocha M, Fizames C, Fort S, Gaillard I, Maillol V, Danchin EGJ, Rouached H, Samain E, Su YH, Thouin J, Touraine B, Puppo A, Frachisse JM, Pauly N, Sentenac H. Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks. FRONTIERS IN PLANT SCIENCE 2016; 7:794. [PMID: 27375649 PMCID: PMC4894911 DOI: 10.3389/fpls.2016.00794] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/22/2016] [Indexed: 05/18/2023]
Abstract
Root hairs are involved in water and nutrient uptake, and thereby in plant autotrophy. In legumes, they also play a crucial role in establishment of rhizobial symbiosis. To obtain a holistic view of Medicago truncatula genes expressed in root hairs and of their regulation during the first hours of the engagement in rhizobial symbiotic interaction, a high throughput RNA sequencing on isolated root hairs from roots challenged or not with lipochitooligosaccharides Nod factors (NF) for 4 or 20 h was carried out. This provided a repertoire of genes displaying expression in root hairs, responding or not to NF, and specific or not to legumes. In analyzing the transcriptome dataset, special attention was paid to pumps, transporters, or channels active at the plasma membrane, to other proteins likely to play a role in nutrient ion uptake, NF electrical and calcium signaling, control of the redox status or the dynamic reprogramming of root hair transcriptome induced by NF treatment, and to the identification of papilionoid legume-specific genes expressed in root hairs. About 10% of the root hair expressed genes were significantly up- or down-regulated by NF treatment, suggesting their involvement in remodeling plant functions to allow establishment of the symbiotic relationship. For instance, NF-induced changes in expression of genes encoding plasma membrane transport systems or disease response proteins indicate that root hairs reduce their involvement in nutrient ion absorption and adapt their immune system in order to engage in the symbiotic interaction. It also appears that the redox status of root hair cells is tuned in response to NF perception. In addition, 1176 genes that could be considered as "papilionoid legume-specific" were identified in the M. truncatula root hair transcriptome, from which 141 were found to possess an ortholog in every of the six legume genomes that we considered, suggesting their involvement in essential functions specific to legumes. This transcriptome provides a valuable resource to investigate root hair biology in legumes and the roles that these cells play in rhizobial symbiosis establishment. These results could also contribute to the long-term objective of transferring this symbiotic capacity to non-legume plants.
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Affiliation(s)
- Isabelle Damiani
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Alice Drain
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Marjorie Guichard
- Institute for Integrative Biology of the Cell, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-SaclayGif sur Yvette, France
| | - Sandrine Balzergue
- POPS Transcriptomic Platform, Centre National de la Recherche Scientifique, Institute of Plant Sciences Paris-Saclay, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-SaclayOrsay, France
- POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay, Paris DiderotOrsay, France
| | - Alexandre Boscari
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Jean-Christophe Boyer
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Véronique Brunaud
- POPS Transcriptomic Platform, Centre National de la Recherche Scientifique, Institute of Plant Sciences Paris-Saclay, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-SaclayOrsay, France
- POPS Transcriptomic Platform, Institute of Plant Sciences Paris-Saclay, Paris DiderotOrsay, France
| | - Sylvain Cottaz
- Université Grenoble Alpes, CERMAVGrenoble, France
- Centre National de la Recherche Scientifique, CERMAVGrenoble, France
| | - Corinne Rancurel
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Martine Da Rocha
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Cécile Fizames
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Sébastien Fort
- Université Grenoble Alpes, CERMAVGrenoble, France
- Centre National de la Recherche Scientifique, CERMAVGrenoble, France
| | - Isabelle Gaillard
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Vincent Maillol
- Université Grenoble Alpes, CERMAVGrenoble, France
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier and Institut de Biologie Computationnelle, Centre National de la Recherche Scientifique and Université MontpellierMontpellier, France
| | - Etienne G. J. Danchin
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Hatem Rouached
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Eric Samain
- Université Grenoble Alpes, CERMAVGrenoble, France
- Centre National de la Recherche Scientifique, CERMAVGrenoble, France
| | - Yan-Hua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Julien Thouin
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Bruno Touraine
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
| | - Alain Puppo
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
| | - Jean-Marie Frachisse
- Institute for Integrative Biology of the Cell, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-SaclayGif sur Yvette, France
| | - Nicolas Pauly
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR 1355-7254 Institut Sophia Agrobiotech, Université Nice Sophia AntipolisSophia Antipolis, France
- *Correspondence: Nicolas Pauly
| | - Hervé Sentenac
- Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche AgronomiqueMontpellier, France
- Hervé Sentenac
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16
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Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Aldrich JT, Paša-Tolić L, Stacey G. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. FRONTIERS IN PLANT SCIENCE 2016; 7:517. [PMID: 27200004 PMCID: PMC4843095 DOI: 10.3389/fpls.2016.00517] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/01/2016] [Indexed: 05/19/2023]
Abstract
Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. In this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identified 1849 and 3091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified 10 key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 h of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. The data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.
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Affiliation(s)
- Oswaldo Valdés-López
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
- Laboratorio de Genómica Funcional de Leguminosas, FES Iztacala Universidad Nacional Autónoma de MéxicoMéxico, Mexico
| | - Josef Batek
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Nicolas Gomez-Hernandez
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Cuong T. Nguyen
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, FES Iztacala Universidad Nacional Autónoma de MéxicoMéxico, Mexico
| | - Ning Zhang
- C.S. Bond Life Sciences Center, Informatics Institute, University of MissouriColumbia, MO, USA
| | - Trupti Joshi
- C.S. Bond Life Sciences Center, Informatics Institute, University of MissouriColumbia, MO, USA
- Department of Computer Science, University of MissouriColumbia, MO, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of MissouriColumbia, MO, USA
| | - Dong Xu
- C.S. Bond Life Sciences Center, Informatics Institute, University of MissouriColumbia, MO, USA
- Department of Computer Science, University of MissouriColumbia, MO, USA
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Karl K. Weitz
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Joshua T. Aldrich
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Gary Stacey
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
- *Correspondence: Gary Stacey
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