1
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Cheng J, Wang J, Bi S, Li M, Wang L, Wang L, Li T, Zhang X, Gao Y, Zhu L, Wang C. GLABRA 2 regulates ETHYLENE OVERPRODUCER 1 accumulation during nutrient deficiency-induced root hair growth. PLANT PHYSIOLOGY 2024:kiae129. [PMID: 38497551 DOI: 10.1093/plphys/kiae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/10/2024] [Indexed: 03/19/2024]
Abstract
Root hairs (RHs), extensive structures of root epidermal cells, are important for plant nutrient acquisition, soil anchorage, and environmental interactions. Excessive production of the phytohormone ethylene (ET) leads to substantial root hair growth, manifested as tolerance to plant nutrient deficiencies. However, the molecular basis of ET production during root hair growth in response to nutrient starvation remains unknown. Herein, we found that a critical transcription factor, GLABRA 2 (GL2), inhibits ET production during root hair growth in Arabidopsis (Arabidopsis thaliana). GL2 directly binds to the promoter of the gene encoding ET OVERPRODUCER 1 (ETO1), one of the most important ET-production-regulation factors, in vitro and in vivo, and then regulates the accumulation and function of ETO1 in root hair growth. The GL2-regulated-ETO1 module is required for promoting root hair growth under nitrogen, phosphorus, or potassium deficiency. Genome-wide analysis revealed numerous genes, such as ROOT HAIR DEFECTIVE 6-LIKE 4, ETHYLENE-INSENSITIVE 3-LIKE 2, ROOT HAIR SPECIFIC 13, are involved in the GL2-regulated-ETO1 module. Our work reveals a key transcription mechanism in the control of ET production during root hair growth under three major nutrient deficiencies.
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Affiliation(s)
- Jianing Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Jinshu Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuangtian Bi
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingyang Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lina Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lu Wang
- Institute of Germplasm Resource and Biotechnology; Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin 300392, China
| | - Tong Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaolan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yue Gao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Che Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
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2
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Zeng Y, Somers J, Bell HS, Dawe RK, Fowler JE, Nelms B, Gent JI. Potent pollen gene regulation by DNA glycosylases in maize. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580204. [PMID: 38405940 PMCID: PMC10888782 DOI: 10.1101/2024.02.13.580204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Although DNA methylation primarily represses transposable elements (TEs) in plants, it also represses select endosperm and pollen genes. These genes, or their cis-regulatory elements, are methylated in plant body tissues but are demethylated by DNA glycosylases (DNGs) in endosperm and pollen, enabling their transcription. Activity of either one of two DNGs, MDR1 or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen segregating mutations in both genes, we identified 58 candidate DNG target genes, whose expression is strongly decreased in double mutant pollen (124-fold decrease on average). These genes account for 11.1% of the wild-type pollen polyadenylated transcriptome, but they are silent or barely detectable in the plant body. They are unusual in their tendency to lack introns but even more so in their having TE-like methylation in their coding DNA sequence. Moreover, they are strongly enriched for predicted functions in cell wall modification. While some may support development of the pollen grain cell wall, expansins and pectinases in this set of genes suggest a function in cell wall loosening to support the rapid tip growth characteristic of pollen tubes as they carry the sperm cells through maternal apoplast and extracellular matrix of the pistil. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with potential for extremely high expression in pollen but constitutive silencing elsewhere.
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Affiliation(s)
- Yibing Zeng
- University of Georgia, Department of Genetics, Athens, GA 30602
| | - Julian Somers
- University of Georgia, Department of Genetics, Athens, GA 30602
| | - Harrison S Bell
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - R Kelly Dawe
- University of Georgia, Department of Genetics, Athens, GA 30602
- University of Georgia, Department of Plant Biology, Athens, GA 30602
| | - John E Fowler
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Brad Nelms
- University of Georgia, Department of Plant Biology, Athens, GA 30602
| | - Jonathan I Gent
- University of Georgia, Department of Plant Biology, Athens, GA 30602
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3
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Guo H, Zhang G, Zhou M, Wan M, Zhu B, Yang Z, Zeng D, Zeng Z. Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs in Aegilops tauschii. Front Genet 2023; 14:1241201. [PMID: 37560386 PMCID: PMC10407559 DOI: 10.3389/fgene.2023.1241201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Abstract
Polyploidization plays important roles in the evolution and breeding of the common wheat. Aegilops tauschii, the D-genome progenitor of the common wheat, provides a valuable pool of resistance genes to multiple diseases. Extensive studies focus on the exploration of these genes for wheat improvement. However, few studies have unveiled alternations on genome-wide expression pattern and histone modifications induced by whole-genome doubling (WGD) process. In this study, we conducted transcriptome analysis for the diploid and tetraploid Ae. taushcii lines using the leaf and root tissues. Both lines tend to display similar tissue-specific pattern. Interestingly, we found that TEs located in genic regions were depleted of the repressive histone mark H3K27me3, whereas their adjacent chromatin was enriched with H3K27me3. The tetraploid line exhibited higher levels of H3K27me3 in those regions than the diploid line, particularly for genic regions associated with TEs of the long interspersed nuclear elements (LINEs), CACTA, PIF/Harbinger, Tc1/Mariner and unclassed DNA transposon. Surprisingly, the expression levels of these TEs cognate genes were negatively associated with the levels of H3K27me3 between the tetraploid and diploid lines, suggesting the five types of TEs located within genic regions might be involved in the regulation of the ploidy-related gene expression, possibly through differential enrichment of H3K27me3 in the genic regions. These findings will help to understand the potential role of specific types of TEs on transcription in response to WGD.
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Affiliation(s)
- Hongwei Guo
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Min Zhou
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Min Wan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
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4
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Wang L, Lin Z, Carli J, Gladala‐Kostarz A, Davies JM, Franklin‐Tong VE, Bosch M. Depletion plays a pivotal role in self-incompatibility, revealing a link between cellular energy status, cytosolic acidification and actin remodelling in pollen tubes. THE NEW PHYTOLOGIST 2022; 236:1691-1707. [PMID: 35775998 PMCID: PMC9796540 DOI: 10.1111/nph.18350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 06/08/2023]
Abstract
Self-incompatibility (SI) involves specific interactions during pollination to reject incompatible ('self') pollen, preventing inbreeding in angiosperms. A key event observed in pollen undergoing the Papaver rhoeas SI response is the formation of punctate F-actin foci. Pollen tube growth is heavily energy-dependent, yet ATP levels in pollen tubes have not been directly measured during SI. Here we used transgenic Arabidopsis lines expressing the Papaver pollen S-determinant to investigate a possible link between ATP levels, cytosolic pH ([pH]cyt ) and alterations to the actin cytoskeleton. We identify for the first time that SI triggers a rapid and significant ATP depletion in pollen tubes. Artificial depletion of ATP triggered cytosolic acidification and formation of actin aggregates. We also identify in vivo, evidence for a threshold [pH]cyt of 5.8 for actin foci formation. Imaging revealed that SI stimulates acidic cytosolic patches adjacent to the plasma membrane. In conclusion, this study provides evidence that ATP depletion plays a pivotal role in SI upstream of programmed cell death and reveals a link between the cellular energy status, cytosolic acidification and alterations to the actin cytoskeleton in regulating Papaver SI in pollen tubes.
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Affiliation(s)
- Ludi Wang
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityPlas GogerddanAberystwythSY23 3EEUK
| | - Zongcheng Lin
- Key Laboratory of Horticultural Plant BiologyHuazhong Agricultural UniversityWuhan430070China
| | - José Carli
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityPlas GogerddanAberystwythSY23 3EEUK
| | - Agnieszka Gladala‐Kostarz
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityPlas GogerddanAberystwythSY23 3EEUK
| | - Julia M. Davies
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Vernonica E. Franklin‐Tong
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityPlas GogerddanAberystwythSY23 3EEUK
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5
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Cui X, Wang S, Huang Y, Ding X, Wang Z, Zheng L, Bi Y, Ge F, Zhu L, Yuan M, Yalovsky S, Fu Y. Arabidopsis SYP121 acts as an ROP2 effector in the regulation of root hair tip growth. MOLECULAR PLANT 2022; 15:1008-1023. [PMID: 35488430 DOI: 10.1016/j.molp.2022.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 04/04/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Tip growth is an extreme form of polarized cell expansion that occurs in all eukaryotic kingdoms to generate highly elongated tubular cells with specialized functions, including fungal hyphae, animal neurons, plant pollen tubes, and root hairs (RHs). RHs are tubular structures that protrude from the root epidermis to facilitate water and nutrient uptake, microbial interactions, and plant anchorage. RH tip growth requires polarized vesicle targeting and active exocytosis at apical growth sites. However, how apical exocytosis is spatially and temporally controlled during tip growth remains elusive. Here, we report that the Qa-Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) SYP121 acts as an effector of Rho of Plants 2 (ROP2), mediating the regulation of RH tip growth. We show that active ROP2 promotes SYP121 targeting to the apical plasma membrane. Moreover, ROP2 directly interacts with SYP121 and promotes the interaction between SYP121 and the R-SNARE VAMP722 to form a SNARE complex, probably by facilitating the release of the Sec1/Munc18 protein SEC11, which suppresses the function of SYP121. Thus, the ROP2-SYP121 pathway facilitates exocytic trafficking during RH tip growth. Our study uncovers a direct link between an ROP GTPase and vesicular trafficking and a new mechanism for the control of apical exocytosis, whereby ROP GTPase signaling spatially regulates SNARE complex assembly and the polar distribution of a Q-SNARE.
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Affiliation(s)
- Xiankui Cui
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuwei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaohui Huang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xuening Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zirong Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lidan Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yujing Bi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fanghui Ge
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Ming Yuan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaul Yalovsky
- Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China.
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6
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Wang J, Yu YC, Li Y, Chen LQ. Hexose transporter SWEET5 confers galactose sensitivity to Arabidopsis pollen germination via a galactokinase. PLANT PHYSIOLOGY 2022; 189:388-401. [PMID: 35188197 PMCID: PMC9070816 DOI: 10.1093/plphys/kiac068] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/15/2022] [Indexed: 05/12/2023]
Abstract
Galactose is an abundant and essential sugar used for the biosynthesis of many macromolecules in different organisms, including plants. Galactose metabolism is tightly and finely controlled, since excess galactose and its derivatives are inhibitory to plant growth. In Arabidopsis (Arabidopsis thaliana), root growth and pollen germination are strongly inhibited by excess galactose. However, the mechanism of galactose-induced inhibition during pollen germination remains obscure. In this study, we characterized a plasma membrane-localized transporter, Arabidopsis Sugars Will Eventually be Exported Transporter 5, that transports glucose and galactose. SWEET5 protein levels started to accumulate at the tricellular stage of pollen development and peaked in mature pollen, before rapidly declining after pollen germinated. SWEET5 levels are responsible for the dosage-dependent sensitivity to galactose, and galactokinase is essential for these inhibitory effects during pollen germination. However, sugar measurement results indicate that galactose flux dynamics and sugar metabolism, rather than the steady-state galactose level, may explain phenotypic differences between sweet5 and Col-0 in galactose inhibition of pollen germination.
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Affiliation(s)
- Jiang Wang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ya-Chi Yu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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7
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Chhajed S, Lu LL, Mangual G, Zhu W, Dufresne C, Chen S. Three-in-one method for high throughput plant multi-omics. Methods Enzymol 2022; 683:153-170. [PMID: 37087185 DOI: 10.1016/bs.mie.2022.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Multi-omics has gained momentum over the past few years especially in plant single cell-type analysis as they aim to understand cellular molecular networks across different levels of genetic information flow. For multi-omics sample preparation, molecular extractions performed non-simultaneously create rooms for variation, inaccurate data, waste of limited samples, resources and labor. Here we optimized a protocol for 3-in-1 simultaneous extraction of RNA, metabolites, and proteins from the same single cell-type sample. We adapted a commercially available RNA kit with a few modifications to obtain high quality starting materials for sequencing and LC-MS/MS-based metabolomics and proteomics. RNAs are bound to the column, metabolites were extracted in a polar solvent and proteins are precipitated using acetone. This creates an all-in-one workflow using a standard RNA kit. Little training is required to carry out this protocol as it is simple and easy to use. It may be used with a wide range of plant species and different amounts of starting materials, including single cells.
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8
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Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. NATURE PLANTS 2021; 7:1143-1159. [PMID: 34253868 DOI: 10.1101/2020.10.29.361501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/02/2021] [Indexed: 05/19/2023]
Abstract
The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Camilla Ferrari
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sebastian Proost
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | | | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Christos Michaelidis
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Chandra Shekhar Misra
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Jacob Goldberg
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Mark Johnson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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9
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Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. NATURE PLANTS 2021; 7:1143-1159. [PMID: 34253868 DOI: 10.1038/s41477-021-00958-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/02/2021] [Indexed: 05/22/2023]
Abstract
The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Camilla Ferrari
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sebastian Proost
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | | | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Christos Michaelidis
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Chandra Shekhar Misra
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Jacob Goldberg
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Mark Johnson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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10
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Poidevin L, Forment J, Unal D, Ferrando A. Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth. PLANT, CELL & ENVIRONMENT 2021. [PMID: 33289138 DOI: 10.1101/2020.05.29.122937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant reproduction is one key biological process that is very sensitive to heat stress and, as a result, enhanced global warming becomes a serious threat to agriculture. In this work, we have studied the effects of heat on germinated pollen of Arabidopsis thaliana both at the transcriptional and translational level. We have used a high-resolution ribosome profiling technology to provide a comprehensive study of the transcriptome and the translatome of germinated pollen at permissive and restrictive temperatures. We have found significant down-regulation of key membrane transporters required for pollen tube growth by heat, thus uncovering heat-sensitive targets. A subset of the heat-repressed transporters showed coordinated up-regulation with canonical heat-shock genes at permissive conditions. We also found specific regulations at the translational level and we have uncovered the presence of ribosomes on sequences annotated as non-coding. Our results demonstrate that heat impacts mostly on membrane transporters thus explaining the deleterious effects of heat stress on pollen growth. The specific regulations at the translational level and the presence of ribosomes on non-coding RNAs highlights novel regulatory aspects on plant fertilization.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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11
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Stephan OOH. Implications of ionizing radiation on pollen performance in comparison with diverse models of polar cell growth. PLANT, CELL & ENVIRONMENT 2021; 44:665-691. [PMID: 33124689 DOI: 10.1111/pce.13929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Research concerning the effects of ionizing radiation (IR) on plant systems is essential for numerous aspects of human society, as for instance, in terms of agriculture and plant breeding, but additionally for elucidating consequences of radioactive contamination of the ecosphere. This comprehensive survey analyses effects of x- and γ-irradiation on male gametophytes comprising primarily in vitro but also in vivo data of diverse plant species. The IR-dose range for pollen performance was compiled and 50% inhibition doses (ID50 ) for germination and tube growth were comparatively related to physiological characteristics of the microgametophyte. Factors influencing IR-susceptibility of mature pollen and polarized tube growth were evaluated, such as dose-rate, environmental conditions, or species-related variations. In addition, all available reports suggesting bio-positive IR-effects particularly on pollen performance were examined. Most importantly, for the first time influences of IR specifically on diverse phylogenetic models of polar cell growth were comparatively analysed, and thus demonstrated that the gametophytic system of pollen is extremely resistant to IR, more than plant sporophytes and especially much more than comparable animal cells. Beyond that, this study develops hypotheses regarding a molecular basis for the extreme IR-resistance of the plant microgametophyte and highlights its unique rank among organismal systems.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
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12
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Wang X, Bi S, Wang L, Li H, Gao BA, Huang S, Qu X, Cheng J, Wang S, Liu C, Jiang Y, Zhang B, Liu X, Zhang S, Fu Y, Zhang Z, Wang C. GLABRA2 Regulates Actin Bundling Protein VILLIN1 in Root Hair Growth in Response to Osmotic Stress. PLANT PHYSIOLOGY 2020; 184:176-193. [PMID: 32636342 PMCID: PMC7479883 DOI: 10.1104/pp.20.00480] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/28/2020] [Indexed: 05/04/2023]
Abstract
Actin binding proteins and transcription factors are essential in regulating plant root hair growth in response to various environmental stresses; however, the interaction between these two factors in regulating root hair growth remains poorly understood. Apical and subapical thick actin bundles are necessary for terminating rapid elongation of root hair cells. Here, we show that Arabidopsis (Arabidopsis thaliana) actin-bundling protein Villin1 (VLN1) decorates filaments in shank, subapical, and apical hairs. vln1 mutants displayed significantly longer hairs with longer hair growing time and defects in the thick actin bundles and bundling activities in the subapical and apical regions, whereas seedlings overexpressing VLN1 showed different results. Genetic analysis showed that the transcription factor GLABRA2 (Gl2) played a regulatory role similar to that of VLN1 in hair growth and actin dynamics. Moreover, further analyses demonstrated that VLN1 overexpression suppresses the gl2 mutant phenotypes regarding hair growth and actin dynamics; GL2 directly recognizes the promoter of VLN1 and positively regulates VLN1 expression in root hairs; and the GL2-mediated VLN1 pathway is involved in the root hair growth response to osmotic stress. Our results demonstrate that the GL2-mediated VLN1 pathway plays an important role in the root hair growth response to osmotic stress, and they describe a transcriptional mechanism that regulates actin dynamics and thereby modulates cell tip growth in response to environmental signals.
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Affiliation(s)
- Xianling Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuangtian Bi
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lu Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Hongpeng Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Bi-ao Gao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shanjin Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolu Qu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Horticulture and Forestry, Huazhong Agricultural University, WuHan 430072, China
| | - Jianing Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shucai Wang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Caiyuan Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yikuo Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shaobin Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Che Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
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13
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Jimenez-Jimenez S, Santana O, Lara-Rojas F, Arthikala MK, Armada E, Hashimoto K, Kuchitsu K, Salgado S, Aguirre J, Quinto C, Cárdenas L. Differential tetraspanin genes expression and subcellular localization during mutualistic interactions in Phaseolus vulgaris. PLoS One 2019; 14:e0219765. [PMID: 31437164 PMCID: PMC6705802 DOI: 10.1371/journal.pone.0219765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/01/2019] [Indexed: 12/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi and rhizobia association with plants are two of the most successful plant-microbe associations that allow the assimilation of P and N by plants, respectively. These mutualistic interactions require a molecular dialogue, i.e., legume roots exude flavonoids or strigolactones which induce the Nod factors or Myc factors synthesis and secretion from the rhizobia or fungi, respectively. These Nod or Myc factors trigger several responses in the plant root, including calcium oscillations, and reactive oxygen species (ROS). Furthermore, superoxide and H2O2 have emerged as key components that regulate the transitions from proliferation to differentiation in the plant meristems. Similar to the root meristem, the nodule meristem accumulates superoxide and H2O2. Tetraspanins are transmembrane proteins that organize into tetraspanin web regions, where they recruit specific proteins into platforms required for signal transduction, membrane fusion, cell trafficking and ROS generation. Plant tetraspanins are scaffolding proteins associated with root radial patterning, biotic and abiotic stress responses, cell fate determination, and hormonal regulation and recently have been reported as a specific marker of exosomes in animal and plant cells and key players at the site of plant fungal infection. In this study, we conducted transcriptional profiling of the tetraspanin family in common bean (Phaseolus vulgaris L. var. Negro Jamapa) to determine the specific expression patterns and subcellular localization of tetraspanins during nodulation or under mycorrhizal association. Our results demonstrate that the tetraspanins are transcriptionally modulated during the mycorrhizal association, but are also expressed in the infection thread and nodule meristem development. Subcellular localization indicates that tetraspanins have a key role in vesicular trafficking, cell division, and root hair polar growth.
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Affiliation(s)
- Saul Jimenez-Jimenez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Olivia Santana
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Fernando Lara-Rojas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México, León, Guanajuato, México
| | - Elisabeth Armada
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Kenji Hashimoto
- Department of Applied Biological Science, Tokyo University of Science, Yamazaki, Noda, Chiba, Japan
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, Yamazaki, Noda, Chiba, Japan
| | - Sandra Salgado
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jesús Aguirre
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail:
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14
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Hoffmann RD, Olsen LI, Ezike CV, Pedersen JT, Manstretta R, López-Marqués RL, Palmgren M. Roles of plasma membrane proton ATPases AHA2 and AHA7 in normal growth of roots and root hairs in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2019; 166:848-861. [PMID: 30238999 PMCID: PMC7379730 DOI: 10.1111/ppl.12842] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 05/18/2023]
Abstract
Plasma membrane H+ -ATPase pumps build up the electrochemical H+ gradients that energize most other transport processes into and out of plant cells through channel proteins and secondary active carriers. In Arabidopsis thaliana, the AUTOINHIBITED PLASMA MEMBRANE H+ -ATPases AHA1, AHA2 and AHA7 are predominant in root epidermal cells. In contrast to other H+ -ATPases, we find that AHA7 is autoinhibited by a sequence present in the extracellular loop between transmembrane segments 7 and 8. Autoinhibition of pump activity was regulated by extracellular pH, suggesting negative feedback regulation of AHA7 during establishment of an H+ gradient. Due to genetic redundancy, it has proven difficult to test the role of AHA2 and AHA7, and mutant phenotypes have previously only been observed under nutrient stress conditions. Here, we investigated root and root hair growth under normal conditions in single and double mutants of AHA2 and AHA7. We find that AHA2 drives root cell expansion during growth but that, unexpectedly, restriction of root hair elongation is dependent on AHA2 and AHA7, with each having different roles in this process.
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Affiliation(s)
- Robert D. Hoffmann
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Lene I. Olsen
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Chukwuebuka V. Ezike
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Jesper T. Pedersen
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Raffaele Manstretta
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Rosa L. López-Marqués
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Michael Palmgren
- Department of Plant and Environmental SciencesUniversity of CopenhagenDK‐1871FrederiksbergDenmark
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15
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Cao J, Ye C, Hao G, Dabney-Smith C, Hunt AG, Li QQ. Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:589. [PMID: 31134121 PMCID: PMC6523994 DOI: 10.3389/fpls.2019.00589] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/23/2019] [Indexed: 05/15/2023]
Abstract
Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3'-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root hair cells, non-hair epidermal cells, and whole root tip under cadmium stress were prepared and sequenced. Interestingly, a root hair cell type-specific gene expression under short term cadmium exposure, but not related to the prolonged treatment, was detected. Differentially expressed poly(A) sites were identified, which largely contributed to altered gene expression, and enriched in pentose and glucuronate interconversion pathways as well as phenylpropanoid biosynthesis pathways. Numerous genes with poly(A) site switching were found, particularly for functions in cell wall modification, root epidermal differentiation, and root hair tip growth. Our findings suggest that APA plays a functional role as a potential stress modulator in root hair cells under cadmium treatment.
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Affiliation(s)
- Jingyi Cao
- Department of Biology, Miami University, Oxford, OH, United States
- Cell, Molecular, Structural Biology Graduate Program, Miami University, Oxford, OH, United States
| | - Congting Ye
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guijie Hao
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Carole Dabney-Smith
- Cell, Molecular, Structural Biology Graduate Program, Miami University, Oxford, OH, United States
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States
| | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Qingshun Q. Li
- Department of Biology, Miami University, Oxford, OH, United States
- Cell, Molecular, Structural Biology Graduate Program, Miami University, Oxford, OH, United States
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
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16
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Misra CS, Santos MR, Rafael-Fernandes M, Martins NP, Monteiro M, Becker JD. Transcriptomics of Arabidopsis sperm cells at single-cell resolution. PLANT REPRODUCTION 2019; 32:29-38. [PMID: 30675644 DOI: 10.1007/s00497-018-00355-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 05/22/2023]
Abstract
We present a detailed protocol for isolation of single sperm cells and transcriptome analysis to study variation in gene expression between sperm cells. Male gametophyte development in flowering plants begins with a microspore mother cell, which upon two consecutive cell divisions forms a mature pollen grain containing a vegetative nucleus and two sperm cells. Pollen development is a highly dynamic process, involving changes at both the transcriptome and epigenome levels of vegetative nuclei and the pair of sperm cells that have their own cytoplasm and nucleus. While the overall transcriptome of Arabidopsis pollen development is well documented, studies at single-cell level, in particular of sperm cells, are still lacking. Such studies would be essential to understand whether and how the two sperm cells are transcriptionally different, in particular once the pollen tube grows through the transmitting tissue of the pistil. Here we describe a detailed protocol for isolation of single sperm cells from growing pollen tubes and analysis of their transcriptome.
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Affiliation(s)
- Chandra Shekhar Misra
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Avenida da República, 2780-157, Oeiras, Portugal
| | - Mário R Santos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | | | - Nuno P Martins
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Marta Monteiro
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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17
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Hirano T, Konno H, Takeda S, Dolan L, Kato M, Aoyama T, Higaki T, Takigawa-Imamura H, Sato MH. PtdIns(3,5)P 2 mediates root hair shank hardening in Arabidopsis. NATURE PLANTS 2018; 4:888-897. [PMID: 30390081 DOI: 10.1038/s41477-018-0277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/07/2018] [Indexed: 05/27/2023]
Abstract
Root hairs elongate by tip growth and simultaneously harden the shank by constructing the inner secondary cell wall layer. While much is known about the process of tip growth1, almost nothing is known about the mechanism by which root hairs harden the shank. Here we show that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2), the enzymatic product of FORMATION OF APLOID AND BINUCLEATE CELLS 1 (FAB1), is involved in the hardening of the shank in root hairs in Arabidopsis. FAB1 and PtdIns(3,5)P2 localize to the plasma membrane along the shank of growing root hairs. By contrast, phosphatidylinositol 4-phosphate 5-kinase 3 (PIP5K3) and PtdIns(4,5)P2 localize to the apex of the root hair where they are required for tip growth. Reduction of FAB1 function results in the formation of wavy root hairs while those of the wild type are straight. The localization of FAB1 in the plasma membrane of the root hair shank requires the activity of Rho-related GTPases from plants 10 (ROP10) and localization of ROP10 requires FAB1 activity. Computational modelling of root hair morphogenesis successfully reproduces the wavy root hair phenotype. Taken together, these data demonstrate that root hair shank hardening requires PtdIns(3,5)P2/ROP10 signalling.
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Affiliation(s)
- Tomoko Hirano
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Hiroki Konno
- Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Seiji Takeda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture Forestry and Fisheries Technology Center, Kyoto, Japan
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Mariko Kato
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Takumi Higaki
- International Research Organization for Advanced Science and Technology, Kumamoto University Kurokami, Kumamoto, Japan
| | | | - Masa H Sato
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan.
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18
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Moon S, Chandran AKN, An G, Lee C, Jung KH. Genome-wide analysis of root hair-preferential genes in rice. RICE (NEW YORK, N.Y.) 2018; 11:48. [PMID: 30159808 PMCID: PMC6115326 DOI: 10.1186/s12284-018-0241-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 08/10/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Root hairs are valuable in taking up nutrients and water from the rhizosphere and serving as sites of interactions with soil microorganisms. By increasing the external surface area of the roots or interacting with rhizobacteria, root hairs directly and indirectly promote plant growth and yield. Transcriptome data can be used to understand root-hair development in rice. RESULT We performed Agilent 44 K microarray experiments with enriched root-hair samples and identified 409 root hair-preferential genes in rice. The expression patterns of six genes were confirmed using a GUS reporter system and quantitative RT-PCR analysis. Gene Ontology (GO) analysis demonstrated that 13 GO terms, including oxygen transport and cell wall generation, were highly over-represented in those genes. Although comparative analysis between rice and Arabidopsis revealed a large proportion of orthologous pairs, their spatial expression patterns were not conserved. To investigate the molecular network associated with root hair-preferential genes in rice, we analyzed the PPI network as well as coexpression data. Subsequently, we developed a refined network consisting of 24 interactions between 10 genes and 18 of their interactors. CONCLUSION Identification of root hair-preferential genes and in depth analysis of those genes will be a useful reference to accelerate the understanding of root-hair development in rice.
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Affiliation(s)
- Sunok Moon
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Anil Kumar Nalini Chandran
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Gynheung An
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Chanhui Lee
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin, 17104, Korea.
| | - Ki-Hong Jung
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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19
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Libault M, Pingault L, Zogli P, Schiefelbein J. Plant Systems Biology at the Single-Cell Level. TRENDS IN PLANT SCIENCE 2017; 22:949-960. [PMID: 28970001 DOI: 10.1016/j.tplants.2017.08.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/14/2017] [Accepted: 08/21/2017] [Indexed: 05/19/2023]
Abstract
Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.
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Affiliation(s)
- Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Lise Pingault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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20
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Slane D, Reichardt I, El Kasmi F, Bayer M, Jürgens G. Evolutionarily diverse SYP1 Qa-SNAREs jointly sustain pollen tube growth in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:375-385. [PMID: 28792633 DOI: 10.1111/tpj.13659] [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] [Received: 03/24/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 05/08/2023]
Abstract
Intracellular membrane fusion is effected by SNARE proteins that reside on adjacent membranes and form bridging trans-SNARE complexes. Qa-SNARE members of the Arabidopsis SYP1 family are involved in membrane fusion at the plasma membrane or during cell plate formation. Three SYP1 family members have been classified as pollen-specific as inferred from gene expression profiling studies, and two of them, SYP124 and SYP125, are confined to angiosperms. The SYP124 gene appears genetically unstable, whereas its sister gene SYP125 shows essentially no variation among Arabidopsis accessions. The third pollen-specific member SYP131 is sister to SYP132, which appears evolutionarily conserved in the plant lineage. Although evolutionarily diverse, the three SYP1 proteins are functionally overlapping in that only the triple mutant syp124 syp125 syp131 shows a specific and severe male gametophytic defect. While pollen development and germination appear normal, pollen tube growth is arrested during passage through the style. Our results suggest that angiosperm pollen tubes employ a combination of ancient and modern Qa-SNARE proteins to sustain their growth-promoting membrane dynamics during the reproductive process.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Ilka Reichardt
- ZMBP, Developmental Genetics, University of Tübingen, 72076, Tübingen, Germany
| | - Farid El Kasmi
- ZMBP, Developmental Genetics, University of Tübingen, 72076, Tübingen, Germany
| | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
- ZMBP, Developmental Genetics, University of Tübingen, 72076, Tübingen, Germany
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21
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Conze LL, Berlin S, Le Bail A, Kost B. Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes. BMC Genomics 2017; 18:581. [PMID: 28784084 PMCID: PMC5545845 DOI: 10.1186/s12864-017-3972-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 07/31/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Pollen tube growth is essential for plant reproduction and represents a widely employed model to investigate polarized cell expansion, a process important for plant morphogenesis and development. Cellular and regulatory mechanisms underlying pollen tube elongation are under intense investigation, which stands to greatly benefit from a comprehensive understanding of global gene expression profiles in pollen and pollen tubes. Here, RNA sequencing technology was applied to de novo assemble a Nicotiana tabacum male gametophytic transcriptome and to compare transcriptome profiles at two different stages of gametophyte development: mature pollen grains (MPG) and pollen tubes grown for six hours in vitro (PT6). RESULTS De novo assembly of data obtained by 454 sequencing of a normalized cDNA library representing tobacco pollen and pollen tube mRNA (pooled mRNA isolated from mature pollen grains [MPG] and from pollen tubes grown in vitro for 3 [PT3] or 6 [PT6] hours) resulted in the identification of 78,364 unigenes. Among these unigenes, which mapped to 24,933 entries in the Sol Genomics Network (SGN) N. tabacum unigene database, 24,672 were predicted to represent full length cDNAs. In addition, quantitative analyses of data obtained by Illumina sequencing of two separate non-normalized MPG and PT6 cDNA libraries showed that 8979 unigenes were differentially expressed (differentially expressed unigenes: DEGs) between these two developmental stages at a FDR q-value of <0.0001. Interestingly, whereas most of these DEGs were downregulated in PT6, the minor fraction of DEGs upregulated in PT6 was enriched for GO (gene ontology) functions in pollen tube growth or fertilization. CONCLUSIONS A major output of our study is the development of two different high-quality databases representing the tobacco male gametophytic transcriptome and containing encompassing information about global changes in gene expression after pollen germination. Quantitative analyses of these databases 1) indicated that roughly 30% of all tobacco genes are expressed in the male gametophyte, and 2) support previous observations suggesting a global reduction of transcription after pollen germination. Interestingly, a small number of genes, many of which predicted to function in pollen tube growth or fertilization, were found to be upregulated in elongating pollen tubes despite globally reduced transcription.
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Affiliation(s)
- Lei Liu Conze
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Aude Le Bail
- Cell Biology Division, Department of Biology, Friedrich Alexander University, Erlangen/Nuremberg, Germany
| | - Benedikt Kost
- Cell Biology Division, Department of Biology, Friedrich Alexander University, Erlangen/Nuremberg, Germany
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22
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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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23
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Huang L, Shi X, Wang W, Ryu KH, Schiefelbein J. Diversification of Root Hair Development Genes in Vascular Plants. PLANT PHYSIOLOGY 2017; 174:1697-1712. [PMID: 28487476 PMCID: PMC5490906 DOI: 10.1104/pp.17.00374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/30/2017] [Indexed: 05/04/2023]
Abstract
The molecular genetic program for root hair development has been studied intensively in Arabidopsis (Arabidopsis thaliana). To understand the extent to which this program might operate in other plants, we conducted a large-scale comparative analysis of root hair development genes from diverse vascular plants, including eudicots, monocots, and a lycophyte. Combining phylogenetics and transcriptomics, we discovered conservation of a core set of root hair genes across all vascular plants, which may derive from an ancient program for unidirectional cell growth coopted for root hair development during vascular plant evolution. Interestingly, we also discovered preferential diversification in the structure and expression of root hair development genes, relative to other root hair- and root-expressed genes, among these species. These differences enabled the definition of sets of genes and gene functions that were acquired or lost in specific lineages during vascular plant evolution. In particular, we found substantial divergence in the structure and expression of genes used for root hair patterning, suggesting that the Arabidopsis transcriptional regulatory mechanism is not shared by other species. To our knowledge, this study provides the first comprehensive view of gene expression in a single plant cell type across multiple species.
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Affiliation(s)
- Ling Huang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Xinhui Shi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Wenjia Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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24
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Wege S, Gilliham M, Henderson SW. Chloride: not simply a 'cheap osmoticum', but a beneficial plant macronutrient. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3057-3069. [PMID: 28379459 DOI: 10.1093/jxb/erx050] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
At macronutrient levels, chloride has positive effects on plant growth, which are distinct from its function in photosynthesis..
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Affiliation(s)
- Stefanie Wege
- Australian Research Council Centre of Excellence in Plant Energy Biology & The University of Adelaide, School of Agriculture, Food and Wine, Waite Research Precinct, PMB1, Glen Osmond, South Australia 5064, Australia
| | - Matthew Gilliham
- Australian Research Council Centre of Excellence in Plant Energy Biology & The University of Adelaide, School of Agriculture, Food and Wine, Waite Research Precinct, PMB1, Glen Osmond, South Australia 5064, Australia
| | - Sam W Henderson
- Australian Research Council Centre of Excellence in Plant Energy Biology & The University of Adelaide, School of Agriculture, Food and Wine, Waite Research Precinct, PMB1, Glen Osmond, South Australia 5064, Australia
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25
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Moro CF, Gaspar M, da Silva FR, Pattathil S, Hahn MG, Salgado I, Braga MR. S-nitrosoglutathione promotes cell wall remodelling, alters the transcriptional profile and induces root hair formation in the hairless root hair defective 6 (rhd6) mutant of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2017; 213:1771-1786. [PMID: 27880005 DOI: 10.1111/nph.14309] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
Nitric oxide (NO) exerts pleiotropic effects on plant development; however, its involvement in cell wall modification during root hair formation (RHF) has not yet been addressed. Here, mutants of Arabidopsis thaliana with altered root hair phenotypes were used to assess the involvement of S-nitrosoglutathione (GSNO), the primary NO source, in cell wall dynamics and gene expression in roots induced to form hairs. GSNO and auxin restored the root hair phenotype of the hairless root hair defective 6 (rhd6) mutant. A positive correlation was observed between increased NO production and RHF induced by auxin in rhd6 and transparent testa glabra (ttg) mutants. Deposition of an epitope within rhamnogalacturonan-I recognized by the CCRC-M2 antibody was delayed in root hair cells (trichoblasts) compared with nonhair cells (atrichoblasts). GSNO, but not auxin, restored the wild-type root glycome and transcriptome profiles in rhd6, modulating the expression of a large number of genes related to cell wall composition and metabolism, as well as those encoding ribosomal proteins, DNA and histone-modifying enzymes and proteins involved in post-translational modification. Our results demonstrate that NO plays a key role in cell wall remodelling in trichoblasts and suggest that it also participates in chromatin modification in root cells of A. thaliana.
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Affiliation(s)
- Camila Fernandes Moro
- Programa de Pós-Graduação em Biologia Celular e Estrutural, Universidade Estadual de Campinas, Campinas, SP, 13083-865, Brazil
| | - Marilia Gaspar
- Núcleo de Pesquisa em Fisiologia e Bioquímica, Instituto de Botânica, São Paulo, SP, 04301-012, Brazil
| | | | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602-4712, USA
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602-4712, USA
| | - Ione Salgado
- Núcleo de Pesquisa em Fisiologia e Bioquímica, Instituto de Botânica, São Paulo, SP, 04301-012, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, Campinas, SP, 13083-970, Brazil
| | - Marcia Regina Braga
- Núcleo de Pesquisa em Fisiologia e Bioquímica, Instituto de Botânica, São Paulo, SP, 04301-012, Brazil
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26
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Schoenaers S, Balcerowicz D, Costa A, Vissenberg K. The Kinase ERULUS Controls Pollen Tube Targeting and Growth in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1942. [PMID: 29184563 PMCID: PMC5694544 DOI: 10.3389/fpls.2017.01942] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/27/2017] [Indexed: 05/09/2023]
Abstract
In this paper, we describe the role of the receptor-like kinase ERULUS (ERU) in PT growth of Arabidopsis thaliana. In silico analysis and transcriptional reporter lines revealed that ERU is only expressed in pollen and root hairs (RHs), making it a tip growth-specific kinase. Deviations from Mendelian inheritance were observed in the offspring of self-pollinated heterozygous eru plants. We found that in vivo eru PT targeting was disturbed, providing a possible explanation for the observed decrease in eru fertilization competitiveness. Extracellular calcium perception and intracellular calcium dynamics lie at the basis of in vivo pollen tube (PT) tip growth and guidance. In vitro, ERU loss-of-function lines displayed no obvious PT phenotype, unless grown on low extracellular calcium ([Ca2+]ext) medium. When grown at 12 the normal [Ca2+]ext, eru PTs grew 37% slower relative to WT PTs. Visualization of cytoplasmic [Ca2+]cyt oscillations using the Yellow Cameleon 3.6 (YC3.6) calcium sensor showed that, unlike in WT PTs, eru apical [Ca2+]cyt oscillations occur at a lower frequency when grown at lower [Ca2+]ext, consistent with the observed reduced growth velocity. Our results show that the tip growth-specific kinase ERULUS is involved in regulating Ca2+-dependent PT growth, and most importantly, fertilization efficiency through successful PT targeting to the ovules.
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Affiliation(s)
- Sébastjen Schoenaers
- Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
| | - Daria Balcerowicz
- Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
| | - Alex Costa
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Biophysics, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Kris Vissenberg
- Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Plant Biochemistry and Biotechnology Lab, Technological Educational Institute of Crete: University of Applied Sciences, Crete, Greece
- *Correspondence: Kris Vissenberg,
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27
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Michard E, Simon AA, Tavares B, Wudick MM, Feijó JA. Signaling with Ions: The Keystone for Apical Cell Growth and Morphogenesis in Pollen Tubes. PLANT PHYSIOLOGY 2017; 173:91-111. [PMID: 27895207 PMCID: PMC5210754 DOI: 10.1104/pp.16.01561] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/19/2016] [Indexed: 05/18/2023]
Abstract
Ion homeostasis and signaling are crucial to regulate pollen tube growth and morphogenesis and affect upstream membrane transporters and downstream targets.
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Affiliation(s)
- Erwan Michard
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815 (E.M., A.A.S., M.M.W., J.A.F.); and
- Instituto Gulbenkian de Ciência, Oeiras 2780-901, Portugal (B.T.)
| | - Alexander A Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815 (E.M., A.A.S., M.M.W., J.A.F.); and
- Instituto Gulbenkian de Ciência, Oeiras 2780-901, Portugal (B.T.)
| | - Bárbara Tavares
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815 (E.M., A.A.S., M.M.W., J.A.F.); and
- Instituto Gulbenkian de Ciência, Oeiras 2780-901, Portugal (B.T.)
| | - Michael M Wudick
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815 (E.M., A.A.S., M.M.W., J.A.F.); and
- Instituto Gulbenkian de Ciência, Oeiras 2780-901, Portugal (B.T.)
| | - José A Feijó
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815 (E.M., A.A.S., M.M.W., J.A.F.); and
- Instituto Gulbenkian de Ciência, Oeiras 2780-901, Portugal (B.T.)
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28
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Wang H, Lan P, Shen RF. Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs. Proteomics 2016; 16:877-93. [PMID: 26749523 DOI: 10.1002/pmic.201500265] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/28/2015] [Accepted: 01/05/2016] [Indexed: 11/11/2022]
Abstract
Plants and other multicellular organisms consist of many types of specialized cells. Systems-wide exploration of large-scale information from singe cell level is essential to understand how cell works. Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species-specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
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29
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Nazemof N, Couroux P, Xing T, Robert LS. Proteomic analysis of the mature Brassica stigma reveals proteins with diverse roles in vegetative and reproductive development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 250:51-58. [PMID: 27457983 DOI: 10.1016/j.plantsci.2016.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
The stigma, the specialized apex of the Brassicaceae gynoecium, plays a role in pollen capture, discrimination, hydration, germination, and guidance. Despite this crucial role in reproduction, the global proteome underlying Brassicaceae stigma development and function remains largely unknown. As a contribution towards the characterization of the Brassicaceae dry stigma global proteome, more than 2500 Brassica napus mature stigma proteins were identified using three different gel-based proteomics approaches. Most stigma proteins participated in Metabolic Processes, Responses to Stimulus or Stress, Cellular or Developmental Processes, and Transport. The stigma was found to express a wide variety of proteins with demonstrated roles in cellular and organ development including proteins known to be involved in cellular expansion and morphogenesis, embryo development, as well as gynoecium and stigma development. Comparisons to a corresponding proteome from a very morphologically different Poaceae dry stigma showed a very similar distribution of proteins among different functional categories, but also revealed evident distinctions in protein composition especially in glucosinolate and carotenoid metabolism, photosynthesis, and self-incompatibility. To our knowledge, this study reports the largest Brassicaceae stigma protein dataset described to date.
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Affiliation(s)
- Nazila Nazemof
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, ON, Canada.
| | - Philippe Couroux
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.
| | - Tim Xing
- Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, ON, Canada.
| | - Laurian S Robert
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.
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30
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Jaborsky M, Maierhofer T, Olbrich A, Escalante-Pérez M, Müller HM, Simon J, Krol E, Cuin TA, Fromm J, Ache P, Geiger D, Hedrich R. SLAH3-type anion channel expressed in poplar secretory epithelia operates in calcium kinase CPK-autonomous manner. THE NEW PHYTOLOGIST 2016; 210:922-33. [PMID: 26831448 DOI: 10.1111/nph.13841] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/03/2015] [Indexed: 05/14/2023]
Abstract
Extrafloral nectaries secrete a sweet sugar cocktail that lures predator insects for protection from foraging herbivores. Apart from sugars and amino acids, the nectar contains the anions chloride and nitrate. Recent studies with Populus have identified a type of nectary covered by apical bipolar epidermal cells, reminiscent of the secretory brush border epithelium in animals. Border epithelia operate transepithelial anion transport, which is required for membrane potential and/or osmotic adjustment of the secretory cells. In search of anion transporters expressed in extrafloral nectaries, we identified PttSLAH3 (Populus tremula × Populus tremuloides SLAC1 Homologue3), an anion channel of the SLAC/SLAH family. When expressed in Xenopus oocytes, PttSLAH3 displayed the features of a voltage-dependent anion channel, permeable to both nitrate and chloride. In contrast to the Arabidopsis SLAC/SLAH family members, the poplar isoform PttSLAH3 is independent of phosphorylation activation by protein kinases. To understand the basis for the autonomous activity of the poplar SLAH3, we generated and expressed chimera between kinase-independent PttSLAH3 and kinase-dependent Arabidopsis AtSLAH3. We identified the N-terminal tail and, to a lesser extent, the C-terminal tail as responsible for PttSLAH3 kinase-(in)dependent action. This feature of PttSLAH3 may provide the secretory cell with a channel probably controlling long-term nectar secretion.
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Affiliation(s)
- Mario Jaborsky
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Tobias Maierhofer
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Andrea Olbrich
- Thünen Institute of Wood Research, Leuschnerstr. 91d, Hamburg, 21031, Germany
| | - María Escalante-Pérez
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Heike M Müller
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Judy Simon
- Chair of Tree Physiology, University of Freiburg, Freiburg, 79110, Germany
| | - Elzbieta Krol
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Tracey Ann Cuin
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Jörg Fromm
- Center for Wood Sciences, University of Hamburg, Leuschnerstr. 91, Hamburg, 21031, Germany
| | - Peter Ache
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Dietmar Geiger
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
| | - Rainer Hedrich
- University Würzburg, Biozentrum, Julius-von-Sachs-Institut für Biowissenschaften, Julius-von-Sachs-Platz 2, Würzburg, D-97082, Germany
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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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Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD. A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants. MOLECULAR PLANT 2016; 9:205-220. [PMID: 26687813 DOI: 10.1016/j.molp.2015.12.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/28/2015] [Accepted: 12/01/2015] [Indexed: 05/08/2023]
Abstract
Identifying the genetic mechanisms that underpin the evolution of new organ and tissue systems is an aim of evolutionary developmental biology. Comparative functional genetic studies between angiosperms and bryophytes can define those genetic changes that were responsible for developmental innovations. Here, we report the generation of a transcriptome atlas covering most phases in the life cycle of the model bryophyte Physcomitrella patens, including detailed sporophyte developmental progression. We identified a comprehensive set of sporophyte-specific transcription factors, and found that many of these genes have homologs in angiosperms that function in developmental processes such as flowering and shoot branching. Deletion of the PpTCP5 transcription factor results in development of supernumerary sporangia attached to a single seta, suggesting that it negatively regulates branching in the moss sporophyte. Given that TCP genes repress branching in angiosperms, we suggest that this activity is ancient. Finally, comparison of P. patens and Arabidopsis thaliana transcriptomes led us to the identification of a conserved core of transcription factors expressed in tip-growing cells. We identified modifications in the expression patterns of these genes that could account for developmental differences between P. patens tip-growing cells and A. thaliana pollen tubes and root hairs.
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Affiliation(s)
- Carlos Ortiz-Ramírez
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | | | - Anna Thamm
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Mingyi Wang
- Division of Plant Biology, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - José A Feijó
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal; Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Building, College Park, MD 20742-5815, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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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: 18] [Impact Index Per Article: 2.3] [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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Salazar-Henao JE, Schmidt W. An Inventory of Nutrient-Responsive Genes in Arabidopsis Root Hairs. FRONTIERS IN PLANT SCIENCE 2016; 7:237. [PMID: 26973680 PMCID: PMC4771725 DOI: 10.3389/fpls.2016.00237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/12/2016] [Indexed: 05/07/2023]
Abstract
Root hairs, single cell extensions of root epidermal cells that are critically involved in the acquisition of mineral nutrients, have proven to be an excellent model system for studying plant cell growth. More recently, omics-based systems biology approaches have extended the model function of root hairs toward functional genomic studies. While such studies are extremely useful to decipher the complex mechanisms underlying root hair morphogenesis, their importance for the performance and fitness of the plant puts root hairs in the spotlight of research aimed at elucidating aspects with more practical implications. Here, we mined transcriptomic and proteomic surveys to catalog genes that are preferentially expressed in root hairs and responsive to nutritional signals. We refer to this group of genes as the root hair trophomorphome. Our analysis shows that the activity of genes within the trophomorphome is regulated at both the transcriptional and post-transcriptional level with the mode of regulation being related to the function of the gene product. A core set of proteins functioning in cell wall modification and protein transport was defined as the backbone of the trophomorphome. In addition, our study shows that homeostasis of reactive oxygen species and redox regulation plays a key role in root hair trophomorphogenesis.
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Affiliation(s)
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
- Biotechnology Center, National Chung-Hsing UniversityTaichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan UniversityTaipei, Taiwan
- *Correspondence: Wolfgang Schmidt
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MacAlister CA, Ortiz-Ramírez C, Becker JD, Feijó JA, Lippman ZB. Hydroxyproline O-arabinosyltransferase mutants oppositely alter tip growth in Arabidopsis thaliana and Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:193-208. [PMID: 26577059 PMCID: PMC4738400 DOI: 10.1111/tpj.13079] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/17/2015] [Accepted: 11/03/2015] [Indexed: 05/20/2023]
Abstract
Hydroxyproline O-arabinosyltransferases (HPATs) are members of a small, deeply conserved family of plant-specific glycosyltransferases that add arabinose sugars to diverse proteins including cell wall-associated extensins and small signaling peptides. Recent genetic studies in flowering plants suggest that different HPAT homologs have been co-opted to function in diverse species-specific developmental contexts. However, nothing is known about the roles of HPATs in basal plants. We show that complete loss of HPAT function in Arabidopsis thaliana and the moss Physcomitrella patens results in a shared defect in gametophytic tip cell growth. Arabidopsis hpat1/2/3 triple knockout mutants suffer from a strong male sterility defect as a consequence of pollen tubes that fail to fully elongate following pollination. Knocking out the two HPAT genes of Physcomitrella results in larger multicellular filamentous networks due to increased elongation of protonemal tip cells. Physcomitrella hpat mutants lack cell-wall associated hydroxyproline arabinosides and can be rescued with exogenous cellulose, while global expression profiling shows that cell wall-associated genes are severely misexpressed, implicating a defect in cell wall formation during tip growth. Our findings point to a major role for HPATs in influencing cell elongation during tip growth in plants.
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Affiliation(s)
| | | | - Jörg D Becker
- Instituto Gulbenkian de Ciência, P-2780-156, Oeiras, Portugal
| | - José A Feijó
- Instituto Gulbenkian de Ciência, P-2780-156, Oeiras, Portugal
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742-5815, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11746, USA
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11746, USA
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36
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Serin EAR, Nijveen H, Hilhorst HWM, Ligterink W. Learning from Co-expression Networks: Possibilities and Challenges. FRONTIERS IN PLANT SCIENCE 2016; 7:444. [PMID: 27092161 PMCID: PMC4825623 DOI: 10.3389/fpls.2016.00444] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 05/18/2023]
Abstract
Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological processes is the discovery of causal genes and regulatory mechanisms controlling these processes. The recent surge of omics data has opened the door to a system-wide understanding of the flow of biological information underlying complex traits. However, dealing with the corresponding large data sets represents a challenging endeavor that calls for the development of powerful bioinformatics methods. A popular approach is the construction and analysis of gene networks. Such networks are often used for genome-wide representation of the complex functional organization of biological systems. Network based on similarity in gene expression are called (gene) co-expression networks. One of the major application of gene co-expression networks is the functional annotation of unknown genes. Constructing co-expression networks is generally straightforward. In contrast, the resulting network of connected genes can become very complex, which limits its biological interpretation. Several strategies can be employed to enhance the interpretation of the networks. A strategy in coherence with the biological question addressed needs to be established to infer reliable networks. Additional benefits can be gained from network-based strategies using prior knowledge and data integration to further enhance the elucidation of gene regulatory relationships. As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes. In this study we review the different approaches for co-expression network inference in plants. We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks. Additionally, we discuss promising bioinformatics approaches that predict networks for specific purposes.
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Affiliation(s)
- Elise A. R. Serin
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
- Laboratory of Bioinformatics, Wageningen UniversityWageningen, Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Wilco Ligterink
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37
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Receptor-like cytoplasmic kinase MARIS functions downstream of CrRLK1L-dependent signaling during tip growth. Proc Natl Acad Sci U S A 2015; 112:12211-6. [PMID: 26378127 DOI: 10.1073/pnas.1512375112] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Growing plant cells need to rigorously coordinate external signals with internal processes. For instance, the maintenance of cell wall (CW) integrity requires the coordination of CW sensing with CW remodeling and biosynthesis to avoid growth arrest or integrity loss. Despite the involvement of receptor-like kinases (RLKs) of the Catharanthus roseus RLK1-like (CrRLK1L) subfamily and the reactive oxygen species-producing NADPH oxidases, it remains largely unknown how this coordination is achieved. ANXUR1 (ANX1) and ANX2, two redundant members of the CrRLK1L subfamily, are required for tip growth of the pollen tube (PT), and their closest homolog, FERONIA, controls root-hair tip growth. Previously, we showed that ANX1 overexpression mildly inhibits PT growth by oversecretion of CW material, whereas pollen tubes of anx1 anx2 double mutants burst spontaneously after germination. Here, we report the identification of suppressor mutants with improved fertility caused by the rescue of anx1 anx2 pollen tube bursting. Mapping of one these mutants revealed an R240C nonsynonymous substitution in the activation loop of a receptor-like cytoplasmic kinase (RLCK), which we named MARIS (MRI). We show that MRI is a plasma membrane-localized member of the RLCK-VIII subfamily and is preferentially expressed in both PTs and root hairs. Interestingly, mri-knockout mutants display spontaneous PT and root-hair bursting. Moreover, expression of the MRI(R240C) mutant, but not its wild-type form, partially rescues the bursting phenotypes of anx1 anx2 PTs and fer root hairs but strongly inhibits wild-type tip growth. Thus, our findings identify a novel positive component of the CrRLK1L-dependent signaling cascade that coordinates CW integrity and tip growth.
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38
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Fehér A, Lajkó DB. Signals fly when kinases meet Rho-of-plants (ROP) small G-proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 237:93-107. [PMID: 26089155 DOI: 10.1016/j.plantsci.2015.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 05/11/2023]
Abstract
Rho-type small GTP-binding plant proteins function as two-state molecular switches in cellular signalling. There is accumulating evidence that Rho-of-plants (ROP) signalling is positively controlled by plant receptor kinases, through the ROP guanine nucleotide exchange factor proteins. These signalling modules regulate cell polarity, cell shape, hormone responses, and pathogen defence, among other things. Other ROP-regulatory proteins might also be subjected to protein phosphorylation by cellular kinases (e.g., mitogen-activated protein kinases or calcium-dependent protein kinases), in order to integrate various cellular signalling pathways with ROP GTPase-dependent processes. In contrast to the role of kinases in upstream ROP regulation, much less is known about the potential link between ROP GTPases and downstream kinase signalling. In other eukaryotes, Rho-type G-protein-activated kinases are widespread and have a key role in many cellular processes. Recent data indicate the existence of structurally different ROP-activated kinases in plants, but their ROP-dependent biological functions still need to be validated. In addition to these direct interactions, ROPs may also indirectly control the activity of mitogen-activated protein kinases or calcium-dependent protein kinases. These kinases may therefore function as upstream as well as downstream kinases in ROP-mediated signalling pathways, such as the phosphatidylinositol monophosphate kinases involved in cell polarity establishment.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Dézi Bianka Lajkó
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary
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Rutley N, Twell D. A decade of pollen transcriptomics. PLANT REPRODUCTION 2015; 28:73-89. [PMID: 25761645 PMCID: PMC4432081 DOI: 10.1007/s00497-015-0261-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/24/2015] [Indexed: 05/19/2023]
Abstract
Overview of pollen transcriptome studies. Pollen development is driven by gene expression, and knowledge of the molecular events underlying this process has undergone a quantum leap in the last decade through studies of the transcriptome. Here, we outline historical evidence for male haploid gene expression and review the wealth of pollen transcriptome data now available. Knowledge of the transcriptional capacity of pollen has progressed from genetic studies to the direct analysis of RNA and from gene-by-gene studies to analyses on a genomic scale. Microarray and/or RNA-seq data can now be accessed for all phases and cell types of developing pollen encompassing 10 different angiosperms. These growing resources have accelerated research and will undoubtedly inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.
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Affiliation(s)
- Nicholas Rutley
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
| | - David Twell
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
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40
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Li W, Lan P. Re-analysis of RNA-seq transcriptome data reveals new aspects of gene activity in Arabidopsis root hairs. FRONTIERS IN PLANT SCIENCE 2015; 6:421. [PMID: 26106402 PMCID: PMC4458573 DOI: 10.3389/fpls.2015.00421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/25/2015] [Indexed: 05/09/2023]
Abstract
Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, interaction with microbe, and in plant anchorage. As a specialized cell type, root hairs, especially in Arabidopsis, provide a pragmatic research system for various aspects of studies. Here, we re-analyzed the RNA-seq transcriptome profile of Arabidopsis root hair cells by Tophat software and used Cufflinks program to mine the differentially expressed genes. Results showed that ERD14, RIN4, AT5G64401 were among the most abundant genes in the root hair cells; while ATGSTU2, AT5G54940, AT4G30530 were highly expressed in non-root hair tissues. In total, 5409 genes, with a fold change greater than two-fold (FDR adjusted P < 0.05), showed differential expression between root hair cells and non-root hair tissues. Of which, 61 were expressed only in root hair cells. One hundred and thirty-six out of 5409 genes have been reported to be "core" root epidermal genes, which could be grouped into nine clusters according to expression patterns. Gene ontology (GO) analysis of the 5409 genes showed that processes of "response to salt stress," "ribosome biogenesis," "protein phosphorylation," and "response to water deprivation" were enriched. Whereas only process of "intracellular signal transduction" was enriched in the subset of 61 genes expressed only in the root hair cells. One hundred and twenty-one unannotated transcripts were identified and 14 of which were shown to be differentially expressed between root hair cells and non-root hair tissues, with transcripts XLOC_000763, XLOC_031361, and XLOC_005665 being highly expressed in the root hair cells. The comprehensive transcriptomic analysis provides new information on root hair gene activity and sets the stage for follow-up experiments to certify the biological functions of the newly identified genes and novel transcripts in root hair cell morphogenesis.
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Affiliation(s)
- Wenfeng Li
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
- *Correspondence: Ping Lan, Institute of Soil Science, Chinese Academy of Sciences, 71# East Beijing Road, Nanjing 210008, China
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41
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Lang V, Usadel B, Obermeyer G. De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species. PLANT MOLECULAR BIOLOGY 2015; 87:69-80. [PMID: 25341867 DOI: 10.1007/s11103-014-0261-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Pollen grains of Lilium longiflorum are a long-established model system for pollen germination and tube tip growth. Due to their size, protein content and almost synchronous germination in synthetic media, they provide a simple system for physiological measurements as well as sufficient material for biochemical studies like protein purifications, enzyme assays, organelle isolation or determination of metabolites during germination and pollen tube elongation. Despite recent progresses in molecular biology techniques, sequence information of expressed proteins or transcripts in lily pollen is still scarce. Using a next generation sequencing strategy (RNAseq), the lily pollen transcriptome was investigated resulting in more than 50 million high quality reads with a length of 90 base pairs. Sequenced transcripts were assembled and annotated, and finally visualized with MAPMAN software tools and compared with other RNAseq or genome data including Arabidopsis pollen, Lilium vegetative tissues and the Amborella trichopoda genome. All lily pollen sequence data are provided as open access files with suitable tools to search sequences of interest.
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Affiliation(s)
- Veronika Lang
- Molecular Plant Biophysics and Biochemistry, Depatment of Molecular Biology, University of Salzburg, Billrothstr.11, 5020, Salzburg, Austria
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42
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Schiefelbein J. Molecular phenotyping of plant single cell-types enhances forward genetic analyses. FRONTIERS IN PLANT SCIENCE 2015; 6:509. [PMID: 26217361 PMCID: PMC4491599 DOI: 10.3389/fpls.2015.00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent advances in the isolation of single cell-types in plants provides an opportunity to conduct detailed analyses of their molecular characteristics at high resolution. This kind of cell-type specific molecular phenotyping is likely to enhance forward genetics studies to dissect the effect of mutations and thereby aid gene function assignment. Recent experimental results support this view, demonstrating that different cell-types exhibit substantial variation in transcript, protein, and metabolite accumulation and these molecular phenotypes are often sensitive to genetic and environmental alterations. The use of single cell-type molecular phenotyping approach to define plant gene function is most amenable to cell-types with well-characterized molecular tools and isolation protocols.
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Affiliation(s)
- John Schiefelbein
- *Correspondence: John Schiefelbein, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109, USA,
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