1
|
Zeng J, Wang Y, Wu G, Sun Q, He X, Zhang X, Sun X, Zhao Y, Liu W, Xu D, Dai X, Ma W. Comparative Transcriptome Analysis Reveals the Genes and Pathways Related to Wheat Root Hair Length. Int J Mol Sci 2024; 25:2069. [PMID: 38396749 PMCID: PMC10889798 DOI: 10.3390/ijms25042069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Tube-like outgrowths from root epidermal cells, known as root hairs, enhance water and nutrient absorption, facilitate microbial interactions, and contribute to plant anchorage by expanding the root surface area. Genetically regulated and strongly influenced by environmental conditions, longer root hairs generally enhance water and nutrient absorption, correlating with increased stress resistance. Wheat, a globally predominant crop pivotal for human nutrition, necessitates the identification of long root hair genotypes and their regulatory genes to enhance nutrient capture and yield potential. This study focused on 261 wheat samples of diverse genotypes during germination, revealing noticeable disparities in the length of the root hair among the genotypes. Notably, two long root hair genotypes (W106 and W136) and two short root hair genotypes (W90 and W100) were identified. Transcriptome sequencing resulted in the development of 12 root cDNA libraries, unveiling 1180 shared differentially expressed genes (DEGs). Further analyses, including GO function annotation, KEGG enrichment, MapMan metabolic pathway analysis, and protein-protein interaction (PPI) network prediction, underscored the upregulation of root hair length regulatory genes in the long root hair genotypes. These included genes are associated with GA and BA hormone signaling pathways, FRS/FRF and bHLH transcription factors, phenylpropanoid, lignin, lignan secondary metabolic pathways, the peroxidase gene for maintaining ROS steady state, and the ankyrin gene with diverse biological functions. This study contributes valuable insights into modulating the length of wheat root hair and identifies candidate genes for the genetic improvement of wheat root traits.
Collapse
Affiliation(s)
- Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yongmei Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Gang Wu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Qingyi Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xinyi Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuelian Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yan Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| |
Collapse
|
2
|
Bawa G, Liu Z, Zhou Y, Fan S, Ma Q, Tissue DT, Sun X. Cotton proteomics: Dissecting the stress response mechanisms in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1035801. [PMID: 36466262 PMCID: PMC9714328 DOI: 10.3389/fpls.2022.1035801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
The natural environment of plants comprises a complex set of biotic and abiotic stresses, and plant responses to these stresses are complex as well. Plant proteomics approaches have significantly revealed dynamic changes in plant proteome responses to stress and developmental processes. Thus, we reviewed the recent advances in cotton proteomics research under changing environmental conditions, considering the progress and challenging factors. Finally, we highlight how single-cell proteomics is revolutionizing plant research at the proteomics level. We envision that future cotton proteomics research at the single-cell level will provide a more complete understanding of cotton's response to stresses.
Collapse
Affiliation(s)
- George Bawa
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Zhixin Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yaping Zhou
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - David T. Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| |
Collapse
|
3
|
Balasubramanian VK, Purvine SO, Liang Y, Kelly RT, Pasa-Tolic L, Chrisler WB, Blumwald E, Stewart CN, Zhu Y, Ahkami AH. Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform. Curr Protoc 2021; 1:e153. [PMID: 34043287 DOI: 10.1002/cpz1.153] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool for studying plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This article describes a recently developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, and ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant leaf and root tissue harvest, sample preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show that the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Plant tissue fixation and embedding Support Protocol 1: Preparation of 2.5% CMC solution Support Protocol 2: Slow freezing of CMC blocks to avoid crack development in the block Basic Protocol 2: Preparation of cryosections Alternate Protocol: Using a vacuum manifold to dehydrate the cryosection slides (primarily for root tissues) Basic Protocol 3: Laser capture microdissection of specific types of plant cells Basic Protocol 4: Nanodroplet-based sample preparation for ultrasensitive proteomic analysis Support Protocol 3: Fabrication of nanowell chips Basic Protocol 5: Liquid chromatography and mass spectrometry.
Collapse
Affiliation(s)
- Vimal K Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, California
| | - C Neal Stewart
- Department of Plant Sciences, Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, Tennessee
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| |
Collapse
|
4
|
Döll S, Djalali Farahani-Kofoet R, Zrenner R, Henze A, Witzel K. Tissue-specific signatures of metabolites and proteins in asparagus roots and exudates. HORTICULTURE RESEARCH 2021; 8:86. [PMID: 33795633 PMCID: PMC8016990 DOI: 10.1038/s41438-021-00510-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/22/2021] [Accepted: 03/01/2021] [Indexed: 05/03/2023]
Abstract
Comprehensive untargeted and targeted analysis of root exudate composition has advanced our understanding of rhizosphere processes. However, little is known about exudate spatial distribution and regulation. We studied the specific metabolite signatures of asparagus root exudates, root outer (epidermis and exodermis), and root inner tissues (cortex and vasculature). The greatest differences were found between exudates and root tissues. In total, 263 non-redundant metabolites were identified as significantly differentially abundant between the three root fractions, with the majority being enriched in the root exudate and/or outer tissue and annotated as 'lipids and lipid-like molecules' or 'phenylpropanoids and polyketides'. Spatial distribution was verified for three selected compounds using MALDI-TOF mass spectrometry imaging. Tissue-specific proteome analysis related root tissue-specific metabolite distributions and rhizodeposition with underlying biosynthetic pathways and transport mechanisms. The proteomes of root outer and inner tissues were spatially very distinct, in agreement with the fundamental differences between their functions and structures. According to KEGG pathway analysis, the outer tissue proteome was characterized by a high abundance of proteins related to 'lipid metabolism', 'biosynthesis of other secondary metabolites' and 'transport and catabolism', reflecting its main functions of providing a hydrophobic barrier, secreting secondary metabolites, and mediating water and nutrient uptake. Proteins more abundant in the inner tissue related to 'transcription', 'translation' and 'folding, sorting and degradation', in accord with the high activity of cortical and vasculature cell layers in growth- and development-related processes. In summary, asparagus root fractions accumulate specific metabolites. This expands our knowledge of tissue-specific plant cell function.
Collapse
Affiliation(s)
- Stefanie Döll
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | | | - Rita Zrenner
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Andrea Henze
- University of Potsdam, Institute of Nutritional Science, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany.
| |
Collapse
|
5
|
Schütz V, Bigler L, Girel S, Laschke L, Sicker D, Schulz M. Conversions of Benzoxazinoids and Downstream Metabolites by Soil Microorganisms. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
6
|
Wang CX, Qi CY, Luo JH, Liu L, He Y, Chen LQ. Characterization of LRL5 as a key regulator of root hair growth in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:71-82. [PMID: 30556198 DOI: 10.1111/tpj.14200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/05/2018] [Accepted: 11/21/2018] [Indexed: 05/27/2023]
Abstract
Root hair, a special type of tubular-shaped cell, outgrows from the root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stresses. Studies in the model plant Arabidopsis have revealed that root-hair initiation and elongation are hierarchically regulated by a group of basic helix-loop-helix (bHLH) transcription factors (TFs). However, knowledge regarding the regulatory pathways of these bHLH TFs in controlling root hair growth remains limited. In this study, RNA-seq analysis was conducted to profile the transcriptome in the elongating maize root hair and >1000 genes with preferential expression in root hair were identified. A consensus cis-element previously featured as the potential bHLH-TF binding sites was present in the regulatory regions for the majority of the root hair-preferentially expressed genes. In addition, an individual change in ZmLRL5, the highest-expressed bHLH-TF in maize root hair resulted in a dramatic reduction in the elongation of root hair, and rendered the growth of root hair hypersensitive to translational inhibition. Moreover, RNA-seq, yeast-one-hybrid and ribosome profile analysis suggested that ZmLRL5 may function as a key player in orchestrating the translational process by directly regulating the expression of translational processes/ribosomal genes during maize root hair growth.
Collapse
Affiliation(s)
- Chun-Xia Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chuang-Ye Qi
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jin-Hong Luo
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Lin Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan He
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Li-Qun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
7
|
Liang Y, Zhu Y, Dou M, Xu K, Chu RK, Chrisler WB, Zhao R, Hixson KK, Kelly RT. Spatially Resolved Proteome Profiling of <200 Cells from Tomato Fruit Pericarp by Integrating Laser-Capture Microdissection with Nanodroplet Sample Preparation. Anal Chem 2018; 90:11106-11114. [PMID: 30118597 DOI: 10.1021/acs.analchem.8b03005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Due to sensitivity limitations, global proteome measurements generally require large amounts of biological starting material, which masks heterogeneity within the samples and differential protein expression among constituent cell types. Methods for spatially resolved proteomics are being developed to resolve protein expression for distinct cell types among highly heterogeneous tissues, but have primarily been applied to mammalian systems. Here we evaluate the performance of cell-type-specific proteome analysis of tomato fruit pericarp tissues by a platform integrating laser-capture microdissection (LCM) and a recently developed automated sample preparation system (nanoPOTS, nanodroplet processing in one pot for trace samples). Tomato fruits were cryosectioned prior to LCM and tissues were dissected and captured directly into nanoPOTS chips for processing. Following processing, samples were analyzed by nanoLC-MS/MS. Approximately 1900 unique peptides and 422 proteins were identified on average from ∼0.04 mm2 tissues comprising ∼8-15 parenchyma cells. Spatially resolved proteome analyses were performed using cells of outer epidermis, collenchyma, and parenchyma. Using ≤200 cells, a total of 1,870 protein groups were identified and the various tissues were easily resolved. The results provide spatial and tissue-specific insights into key enzymes and pathways involved in carbohydrate transport and source-sink relationships in tomato fruit. Of note, at the time of fruit ripening studied here, we identified differentially abundant proteins throughout the pericarp related to chlorophyll biogenesis, photosynthesis, and especially transport.
Collapse
Affiliation(s)
- Yiran Liang
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kerui Xu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - William B Chrisler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kim K Hixson
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| |
Collapse
|
8
|
Jia H, Sun W, Li M, Zhang Z. Integrated Analysis of Protein Abundance, Transcript Level, and Tissue Diversity To Reveal Developmental Regulation of Maize. J Proteome Res 2018; 17:822-833. [DOI: 10.1021/acs.jproteome.7b00586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Haitao Jia
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wei Sun
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manfei Li
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zuxin Zhang
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| |
Collapse
|
9
|
Hochholdinger F, Marcon C, Baldauf JA, Yu P, Frey FP. Proteomics of Maize Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:143. [PMID: 29556242 PMCID: PMC5844967 DOI: 10.3389/fpls.2018.00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.
Collapse
|
10
|
Abstract
Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.
Collapse
Affiliation(s)
- Monika Bansal
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab.,b School of Agriculture , Lovely Professional University , Phagwara 144411 , Punjab
| | - Madhu Sharma
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab
| | - Priyanka Kanwar
- a School of Agriculture, Lovely Professional University , Phagwara 144411 , Punjab
| | - Aakash Goyal
- c Biodiversity and Integrated Gene Management Program , International Center for Agriculture Research in the Dry Areas (ICARDA) , P.O.Box 6299, Rabat-Institutes, Rabat , Morocco
| |
Collapse
|
11
|
Hey S, Baldauf J, Opitz N, Lithio A, Pasha A, Provart N, Nettleton D, Hochholdinger F. Complexity and specificity of the maize (Zea mays L.) root hair transcriptome. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2175-2185. [PMID: 28398587 PMCID: PMC5447894 DOI: 10.1093/jxb/erx104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Root hairs are tubular extensions of epidermis cells. Transcriptome profiling demonstrated that the single cell-type root hair transcriptome was less complex than the transcriptome of multiple cell-type primary roots without root hairs. In total, 831 genes were exclusively and 5585 genes were preferentially expressed in root hairs [false discovery rate (FDR) ≤1%]. Among those, the most significantly enriched Gene Ontology (GO) functional terms were related to energy metabolism, highlighting the high energy demand for the development and function of root hairs. Subsequently, the maize homologs for 138 Arabidopsis genes known to be involved in root hair development were identified and their phylogenetic relationship and expression in root hairs were determined. This study indicated that the genetic regulation of root hair development in Arabidopsis and maize is controlled by common genes, but also shows differences which need to be dissected in future genetic experiments. Finally, a maize root view of the eFP browser was implemented including the root hair transcriptome of the present study and several previously published maize root transcriptome data sets. The eFP browser provides color-coded expression levels for these root types and tissues for any gene of interest, thus providing a novel resource to study gene expression and function in maize roots.
Collapse
Affiliation(s)
- Stefan Hey
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Jutta Baldauf
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Nina Opitz
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| |
Collapse
|
12
|
Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
Collapse
Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Chaturvedi P, Ghatak A, Weckwerth W. Pollen proteomics: from stress physiology to developmental priming. PLANT REPRODUCTION 2016; 29:119-32. [PMID: 27271282 PMCID: PMC4909805 DOI: 10.1007/s00497-016-0283-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/05/2016] [Indexed: 05/19/2023]
Abstract
Pollen development and stress. In angiosperms, pollen or pollen grain (male gametophyte) is a highly reduced two- or three-cell structure which plays a decisive role in plant reproduction. Male gametophyte development takes place in anther locules where diploid sporophytic cells undergo meiotic division followed by two consecutive mitotic processes. A desiccated and metabolically quiescent form of mature pollen is released from the anther which lands on the stigma. Pollen tube growth takes place followed by double fertilization. Apart from its importance in sexual reproduction, pollen is also an interesting model system which integrates fundamental cellular processes like cell division, differentiation, fate determination, polar establishment, cell to cell recognition and communication. Recently, pollen functionality has been studied by multidisciplinary approaches which also include OMICS analyses like transcriptomics, proteomics and metabolomics. Here, we review recent advances in proteomics of pollen development and propose the process of developmental priming playing a key role to guard highly sensitive developmental processes.
Collapse
Affiliation(s)
- Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- School of Biotechnology and Bioinformatics, D.Y. Patil University, Sector No-15, CBD, Belapur, Navi Mumbai, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.
| |
Collapse
|
15
|
Data in support of proteome analysis of gynophores and early swelling pods of peanut (Arachis hypogaea L.). Data Brief 2016; 5:1056-9. [PMID: 26793750 PMCID: PMC4689115 DOI: 10.1016/j.dib.2015.11.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/03/2015] [Accepted: 11/12/2015] [Indexed: 11/20/2022] Open
Abstract
Different from most of other plants, peanut (Arachis hypogaea L.) is a typical geocarpic species which flowering and forming pegs (gynophores) above the ground. Pegs penetrate into soil for embryo and pod development. To investigate the molecular mechanism of geocarpy feature of peanut, the proteome profiles of aerial grown gynophores (S1), subterranean unswollen gynophores (S2), and gynophores that had just started to swell into pods (S3) were analyzed by combining 1 DE with nano LC–MS/MS approaches. The proteomic data provided valuable information for understanding pod development of peanut. The data described here can be found in the PRIDE Archive using the reference number PXD002579-81. A more comprehensive analysis of this data may be obtained from the article in BMC Plant Biology (Zhao et al., 2015 [1]).
Collapse
|
16
|
Schmid MW, Schmidt A, Grossniklaus U. The female gametophyte: an emerging model for cell type-specific systems biology in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:907. [PMID: 26579157 PMCID: PMC4630298 DOI: 10.3389/fpls.2015.00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods ("omics") now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis). Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.
Collapse
Affiliation(s)
| | | | - Ueli Grossniklaus
- Department of Plant & Microbial Biology and Zurich-Basel Plant Science Center, University of ZurichZurich, Switzerland
| |
Collapse
|
17
|
Li Z, Phillip D, Neuhäuser B, Schulze WX, Ludewig U. Protein Dynamics in Young Maize Root Hairs in Response to Macro- and Micronutrient Deprivation. J Proteome Res 2015; 14:3362-71. [DOI: 10.1021/acs.jproteome.5b00399] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zhi Li
- Department
of Plant Systems Biology, University of Hohenheim, Garbenstraße
30, 70599 Stuttgart, Germany
| | - Daniel Phillip
- Institute
of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Benjamin Neuhäuser
- Institute
of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Waltraud X. Schulze
- Department
of Plant Systems Biology, University of Hohenheim, Garbenstraße
30, 70599 Stuttgart, Germany
| | - Uwe Ludewig
- Institute
of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart, Germany
| |
Collapse
|
18
|
Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| |
Collapse
|
19
|
Hossain MS, Joshi T, Stacey G. System approaches to study root hairs as a single cell plant model: current status and future perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:363. [PMID: 26042143 PMCID: PMC4436566 DOI: 10.3389/fpls.2015.00363] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/06/2015] [Indexed: 05/29/2023]
Abstract
Our current understanding of plant functional genomics derives primarily from measurements of gene, protein and/or metabolite levels averaged over the whole plant or multicellular tissues. These approaches risk diluting the response of specific cells that might respond strongly to the treatment but whose signal is diluted by the larger proportion of non-responding cells. For example, if a gene is expressed at a low level, does this mean that it is indeed lowly expressed or is it highly expressed, but only in a few cells? In order to avoid these issues, we adopted the soybean root hair cell, derived from a single, differentiated root epidermal cell, as a single-cell model for functional genomics. Root hair cells are intrinsically interesting since they are major conduits for root water and nutrient uptake and are also the preferred site of infection by nitrogen-fixing rhizobium bacteria. Although a variety of other approaches have been used to study single plant cells or single cell types, the root hair system is perhaps unique in allowing application of the full repertoire of functional genomic and biochemical approaches. In this mini review, we summarize our published work and place this within the broader context of root biology, with a significant focus on understanding the initial events in the soybean-rhizobium interaction.
Collapse
Affiliation(s)
- Md Shakhawat Hossain
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Gary Stacey
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| |
Collapse
|
20
|
Dastmalchi M, Dhaubhadel S. Proteomic insights into synthesis of isoflavonoids in soybean seeds. Proteomics 2015; 15:1646-57. [PMID: 25757747 DOI: 10.1002/pmic.201400444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/25/2014] [Accepted: 12/30/2014] [Indexed: 12/13/2022]
Abstract
Soybean seeds are the major human dietary source of isoflavonoids, a class of plant natural products almost entirely exclusive to legumes. Isoflavonoids reduce the risk of a number of chronic human illnesses. Biosynthesis and accumulation of this class of compounds is a multigenic and complex trait, with a great deal of variability among soybean cultivars and with respect to the environment. There is a wealth of genomic, transcriptomic, and metabolomics data regarding isoflavonoid biosynthesis, but the connection between multigene families and their cognate proteins is a missing link that could provide us with a great deal of functional information. The changing proteome of the developing seed can shed light on the correlative increase in isoflavonoids, while the maternal seed coat proteome can provide the link with inherited metabolic and signaling machinery. In this effort, 'seed-filling' proteomics has revealed key secondary metabolite enzymes that quantitatively vary throughout seed development. Seed coat proteomics has revealed the existence of metabolic apparatus specific to isoflavonoid biosynthesis (isoflavonoid reductase) that could potentially influence the chemical content of this organ. The future of proteomic analysis of isoflavonoid biosynthesis should be centered on the development of quantitative, tissue-specific proteomes that emphasize low-abundance metabolic proteins to extract the whole suite of factors involved.
Collapse
Affiliation(s)
- Mehran Dastmalchi
- Department of Biology, University of Western Ontario, London, Canada
- Southern Crop Protection and Food Research Center, Agriculture and Agri-Food Canada, London, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, London, Canada
- Southern Crop Protection and Food Research Center, Agriculture and Agri-Food Canada, London, Canada
| |
Collapse
|
21
|
Svozil J, Gruissem W, Baerenfaller K. Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues. FRONTIERS IN PLANT SCIENCE 2015; 6:376. [PMID: 26074939 PMCID: PMC4446536 DOI: 10.3389/fpls.2015.00376] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/11/2015] [Indexed: 05/18/2023]
Abstract
Protein and transcript levels are partly decoupled as a function of translation efficiency and protein degradation. Selective protein degradation via the Ubiquitin-26S proteasome system (UPS) ensures protein homeostasis and facilitates adjustment of protein abundance during changing environmental conditions. Since individual leaf tissues have specialized functions, their protein composition is different and hence also protein level regulation is expected to differ. To understand UPS function in a tissue-specific context we developed a method termed Meselect to effectively and rapidly separate Arabidopsis thaliana leaf epidermal, vascular and mesophyll tissues. Epidermal and vascular tissue cells are separated mechanically, while mesophyll cells are obtained after rapid protoplasting. The high yield of proteins was sufficient for tissue-specific proteome analyses after inhibition of the proteasome with the specific inhibitor Syringolin A (SylA) and affinity enrichment of ubiquitylated proteins. SylA treatment of leaves resulted in the accumulation of 225 proteins and identification of 519 ubiquitylated proteins. Proteins that were exclusively identified in the three different tissue types are consistent with specific cellular functions. Mesophyll cell proteins were enriched for plastid membrane translocation complexes as targets of the UPS. Epidermis enzymes of the TCA cycle and cell wall biosynthesis specifically accumulated after proteasome inhibition, and in the vascular tissue several enzymes involved in glucosinolate biosynthesis were found to be ubiquitylated. Our results demonstrate that protein level changes and UPS protein targets are characteristic of the individual leaf tissues and that the proteasome is relevant for tissue-specific functions.
Collapse
Affiliation(s)
| | | | - Katja Baerenfaller
- *Correspondence: Katja Baerenfaller, Plant Biotechnology, Department of Biology, Swiss Federal Institute of Technology Zurich, Zurich Universitaetstrasse 2, 8092 Zurich, Switzerland
| |
Collapse
|
22
|
Nestler J, Liu S, Wen TJ, Paschold A, Marcon C, Tang HM, Li D, Li L, Meeley RB, Sakai H, Bruce W, Schnable PS, Hochholdinger F. Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:729-40. [PMID: 24902980 DOI: 10.1111/tpj.12578] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 05/19/2023]
Abstract
Root hairs are instrumental for nutrient uptake in monocot cereals. The maize (Zea mays L.) roothairless5 (rth5) mutant displays defects in root hair initiation and elongation manifested by a reduced density and length of root hairs. Map-based cloning revealed that the rth5 gene encodes a monocot-specific NADPH oxidase. RNA-Seq, in situ hybridization and qRT-PCR experiments demonstrated that the rth5 gene displays preferential expression in root hairs but also accumulates to low levels in other tissues. Immunolocalization detected RTH5 proteins in the epidermis of the elongation and differentiation zone of primary roots. Because superoxide and hydrogen peroxide levels are reduced in the tips of growing rth5 mutant root hairs as compared with wild-type, and Reactive oxygen species (ROS) is known to be involved in tip growth, we hypothesize that the RTH5 protein is responsible for establishing the high levels of ROS in the tips of growing root hairs required for elongation. Consistent with this hypothesis, a comparative RNA-Seq analysis of 6-day-old rth5 versus wild-type primary roots revealed significant over-representation of only two gene ontology (GO) classes related to the biological functions (i.e. oxidation/reduction and carbohydrate metabolism) among 893 differentially expressed genes (FDR <5%). Within these two classes the subgroups 'response to oxidative stress' and 'cellulose biosynthesis' were most prominently represented.
Collapse
Affiliation(s)
- Josefine Nestler
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Different plant cell types express unique transcriptomes, proteomes, and metabolomes. Therefore, the isolation of specific cell types prior to molecular analyses is important to understand the specification, differentiation, and function of these cells. Isolation of specific plant cell types from composite organs can be achieved by laser microdissection (LMD). A wide variety of methods to fix and embed tissues prior to LMD and downstream molecular analyses have been developed for different plant species and tissues. The present review summarizes and highlights the most recently applied LMD approaches in plant science.
Collapse
Affiliation(s)
- Yvonne Ludwig
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | | |
Collapse
|
24
|
Ischebeck T, Valledor L, Lyon D, Gingl S, Nagler M, Meijón M, Egelhofer V, Weckwerth W. Comprehensive cell-specific protein analysis in early and late pollen development from diploid microsporocytes to pollen tube growth. Mol Cell Proteomics 2014; 13:295-310. [PMID: 24078888 PMCID: PMC3879621 DOI: 10.1074/mcp.m113.028100] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 09/24/2013] [Indexed: 01/10/2023] Open
Abstract
Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At the same time, pollen development is highly sensitive to environmental fluctuations, including temperature, drought, and nutrition. Therefore, pollen biology is a major focus in applied studies and breeding approaches for improving plant productivity in a globally changing climate. The most accessible developmental stages of pollen are the mature pollen and the pollen tubes, and these are thus most frequently analyzed. To reveal a complete quantitative proteome map, we additionally addressed the very early stages, analyzing eight stages of tobacco pollen development: diploid microsporocytes, meiosis, tetrads, microspores, polarized microspores, bipolar pollen, desiccated pollen, and pollen tubes. A protocol for the isolation of the early stages was established. Proteins were extracted and analyzed by means of a new gel LC-MS fractionation protocol. In total, 3817 protein groups were identified. Quantitative analysis was performed based on peptide count. Exceedingly stage-specific differential protein regulation was observed during the conversion from the sporophytic to the gametophytic proteome. A map of highly specialized functionality for the different stages could be revealed from the metabolic activity and pronounced differentiation of proteasomal and ribosomal protein complex composition up to protective mechanisms such as high levels of heat shock proteins in the very early stages of development.
Collapse
Affiliation(s)
- Till Ischebeck
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Luis Valledor
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - David Lyon
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Stephanie Gingl
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Matthias Nagler
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Mónica Meijón
- ¶Gregor-Mendel-Institute for Molecular Plant Biology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Volker Egelhofer
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Wolfram Weckwerth
- From the ‡Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| |
Collapse
|
25
|
Marcon C, Lamkemeyer T, Malik WA, Ungrue D, Piepho HP, Hochholdinger F. Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC–MS. J Proteomics 2013; 93:295-302. [DOI: 10.1016/j.jprot.2013.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/28/2013] [Accepted: 04/11/2013] [Indexed: 01/10/2023]
|
26
|
Abiko M, Furuta K, Yamauchi Y, Fujita C, Taoka M, Isobe T, Okamoto T. Identification of proteins enriched in rice egg or sperm cells by single-cell proteomics. PLoS One 2013; 8:e69578. [PMID: 23936051 PMCID: PMC3723872 DOI: 10.1371/journal.pone.0069578] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/10/2013] [Indexed: 11/19/2022] Open
Abstract
In angiosperms, female gamete differentiation, fertilization, and subsequent zygotic development occur in embryo sacs deeply embedded in the ovaries. Despite their importance in plant reproduction and development, how the egg cell is specialized, fuses with the sperm cell, and converts into an active zygote for early embryogenesis remains unclear. This lack of knowledge is partly attributable to the difficulty of direct analyses of gametes in angiosperms. In the present study, proteins from egg and sperm cells obtained from rice flowers were separated by one-dimensional polyacrylamide gel electrophoresis and globally identified by highly sensitive liquid chromatography coupled with tandem mass spectroscopy. Proteome analyses were also conducted for seedlings, callus, and pollen grains to compare their protein expression profiles to those of gametes. The proteomics data have been deposited to the ProteomeXchange with identifier PXD000265. A total of 2,138 and 2,179 expressed proteins were detected in egg and sperm cells, respectively, and 102 and 77 proteins were identified as preferentially expressed in egg and sperm cells, respectively. Moreover, several rice or Arabidopsis lines with mutations in genes encoding the putative gamete-enriched proteins showed clear phenotypic defects in seed set or seed development. These results suggested that the proteomic data presented in this study are foundational information toward understanding the mechanisms of reproduction and early development in angiosperms.
Collapse
Affiliation(s)
- Mafumi Abiko
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan,
| | - Kensyo Furuta
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan,
| | - Yoshio Yamauchi
- Department of Chemistry, Tokyo Metropolitan University, Tokyo, Japan
| | - Chiharu Fujita
- Department of Chemistry, Tokyo Metropolitan University, Tokyo, Japan
| | - Masato Taoka
- Department of Chemistry, Tokyo Metropolitan University, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Tokyo Metropolitan University, Tokyo, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan,
| |
Collapse
|
27
|
Pechanova O, Takáč T, Šamaj J, Pechan T. Maize proteomics: An insight into the biology of an important cereal crop. Proteomics 2013. [DOI: 10.1002/pmic.201200275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Olga Pechanova
- Mississippi State Chemical Laboratory; Mississippi State University; Mississippi State; MS; USA
| | - Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science; Palacký University; Olomouc; Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science; Palacký University; Olomouc; Czech Republic
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station,; Mississippi State University; Mississippi State; MS; USA
| |
Collapse
|
28
|
Kwasniewski M, Chwialkowska K, Kwasniewska J, Kusak J, Siwinski K, Szarejko I. Accumulation of peroxidase-related reactive oxygen species in trichoblasts correlates with root hair initiation in barley. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:185-95. [PMID: 23218546 DOI: 10.1016/j.jplph.2012.09.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 08/20/2012] [Accepted: 09/11/2012] [Indexed: 05/08/2023]
Abstract
Root hairs are an important model in studies of cell differentiation and development in higher plants. The function of NADPH oxidase-related reactive oxygen species (ROS) in root hair development has been reported extensively in studies on Arabidopsis. In this study, we investigated the mechanism of the initiation of root hair formation, mediated by the peroxidase-dependent production of the highly reactive hydroxyl radical in barley (Hordeum vulgare L.). The distribution of ROS, including the hydroxyl radical (OH) and superoxide (O(2)(-)) was assessed using hydroxyphenyl fluorescein and nitroblue tetrazolium chloride, respectively, in the roots of wild-type plants and two root-hair mutants: root-hairless (rhl1.a) and with root hair growth blocked at the primordium stage (rhp1.b). Peroxidase-dependent OH accumulation was linked to root hair initiation and growth in plants where root hair formation was at least initiated, whereas OH was not detectable in the epidermis of the root-hairless mutant rhl1.a. O(2)(-) distribution in the roots of rhl1.a and rhp1.b mutants was not impaired and did not influence the root hair phenotype. Peroxidase inhibitor treatments of wild-type roots dramatically reduced the ability of growing roots to form root hairs and thus phenocopied the root-hairless phenotype. Expression of two candidate peroxidase genes, HvPRX45 and HvPRX2, was analyzed and their possible role in root hair-specific production of hydroxyl radicals was discussed. We propose a model of a two-step, coordinated ROS formation process in root hair cells that involves root hair-specific peroxidase(s) and root hair-specific NADPH oxidase necessary for a proper root hair formation in barley.
Collapse
Affiliation(s)
- Miroslaw Kwasniewski
- Department of Genetics, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | | | | | | | | | | |
Collapse
|
29
|
Kwasniewski M, Nowakowska U, Szumera J, Chwialkowska K, Szarejko I. iRootHair: a comprehensive root hair genomics database. PLANT PHYSIOLOGY 2013; 161:28-35. [PMID: 23129204 PMCID: PMC3532259 DOI: 10.1104/pp.112.206441] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/01/2012] [Indexed: 05/18/2023]
Abstract
The specialized root epidermis cells of higher plants produce long, tubular outgrowths called root hairs. Root hairs play an important role in nutrient and water uptake, and they serve as a valuable model in studies of plant cell morphogenesis. More than 1,300 articles that describe the biological processes of these unique cells have been published to date. As new fields of root hair research are emerging, the number of new papers published each year and the volumes of new relevant data are continuously increasing. Therefore, there is a general need to facilitate studies on root hair biology by collecting, presenting, and sharing the available information in a systematic, curated manner. Consequently, in this paper, we present a comprehensive database of root hair genomics, iRootHair, which is accessible as a Web-based service. The current version of the database includes information about 153 root hair-related genes that have been identified to date in dicots and monocots along with their putative orthologs in higher plants with sequenced genomes. In order to facilitate the use of the iRootHair database, it is subdivided into interrelated, searchable sections that describe genes, processes of root hair formation, root hair mutants, and available references. The database integrates bioinformatics tools with a focus on sequence identification and annotation. iRootHair is a unique resource for root hair research that integrates the large volume of data related to root hair genomics in a single, curated, and expandable database that is freely available at www.iroothair.org.
Collapse
|
30
|
Brechenmacher L, Nguyen THN, Hixson K, Libault M, Aldrich J, Pasa-Tolic L, Stacey G. Identification of soybean proteins from a single cell type: the root hair. Proteomics 2012; 12:3365-73. [PMID: 22997094 DOI: 10.1002/pmic.201200160] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/18/2012] [Accepted: 08/31/2012] [Indexed: 12/16/2023]
Abstract
Root hairs (RH) are a terminally differentiated single cell type, mainly involved in water and nutrient uptake from the soil. The soybean RH cell represents an excellent model for the study of single cell systems biology. In this study, we identified 5702 proteins, with at least two peptides, from soybean RH using an accurate mass and time tag approach, establishing a comprehensive proteome reference map of this single cell type. We also showed that trypsin is the most appropriate enzyme for soybean proteomic studies by performing an in silico digestion of the soybean proteome using different proteases. Although the majority of proteins identified in this study are involved in basal metabolism, the function of others are more related to RH formation/function and include proteins involved in nutrient uptake (transporters) or vesicular trafficking (cytoskeleton and ras-associated binding proteins). Interestingly, some of these proteins appear to be specifically detected in RH and constitute promising candidates for further studies to elucidate unique features of this single-cell model.
Collapse
Affiliation(s)
- Laurent Brechenmacher
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Dai S, Chen S. Single-cell-type proteomics: toward a holistic understanding of plant function. Mol Cell Proteomics 2012; 11:1622-30. [PMID: 22982375 DOI: 10.1074/mcp.r112.021550] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the protein characteristics of each type of cell will not only reveal specific cell functions, but also enhance understanding of how an organism works. Most plant proteomics studies have focused on using tissues and organs containing a mixture of different cells. Recent single-cell-type proteomics efforts on pollen grains, guard cells, mesophyll cells, root hairs, and trichomes have shown utility. We expect that high resolution proteomic analyses will reveal novel functions in single cells. This review provides an overview of recent developments in plant single-cell-type proteomics. We discuss application of the approach for understanding important cell functions, and we consider the technical challenges of extending the approach to all plant cell types. Finally, we consider the integration of single-cell-type proteomics with transcriptomics and metabolomics with the goal of providing a holistic understanding of plant function.
Collapse
Affiliation(s)
- Shaojun Dai
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | |
Collapse
|
32
|
Janiak A, Piórko S, Matros A, Mock HP, Kwaśniewski M, Chwiałkowska K, Chmielewska B, Szarejko I. A comparative analysis of proteins that accumulate during the initial stage of root hair development in barley root hair mutants and their parent varieties. J Appl Genet 2012; 53:363-76. [PMID: 22847350 PMCID: PMC3477482 DOI: 10.1007/s13353-012-0105-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/15/2012] [Accepted: 07/02/2012] [Indexed: 12/19/2022]
Abstract
The mechanisms of root hair formation have been studied extensively in Arabidopsis but knowledge about these processes in monocot species is still limited, especially in relation to the proteome level. The aim of this study was to identify the proteins that are involved in the initiation and the early stage of root hair tip growth in barley using two-dimensional (2D) electrophoresis and mass spectrometry. A comparison of proteins that accumulate differentially in two root hair mutants and their respective parent varieties resulted in the identification of 13 proteins that take part in several processes related to the root hair morphogenesis, such as the control of vesicular trafficking, ROS signalling and homeostasis, signal transduction by phospholipids metabolism and ATP synthesis. Among the identified proteins, two ATP synthases, two ABC transporters, a small GTPase from the SAR1 family, a PDI-like protein, a monodehydroascorbate reductase, a C2 domain-containing protein and a Wali7 domain-containing protein were found. This study is the first report on the proteins identified in the initial stage of root hair formation in barley and gives new insights into the mechanisms of root hair morphogenesis in a monocot species.
Collapse
Affiliation(s)
- Agnieszka Janiak
- Department of Genetics, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland.
| | | | | | | | | | | | | | | |
Collapse
|