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Song JH, Montes-Luz B, Tadra-Sfeir MZ, Cui Y, Su L, Xu D, Stacey G. High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation. FRONTIERS IN PLANT SCIENCE 2022; 13:820348. [PMID: 35498680 PMCID: PMC9048599 DOI: 10.3389/fpls.2022.820348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Nodule organogenesis in legumes is regulated temporally and spatially through gene networks. Genome-wide transcriptome, proteomic, and metabolomic analyses have been used previously to define the functional role of various plant genes in the nodulation process. However, while significant progress has been made, most of these studies have suffered from tissue dilution since only a few cells/root regions respond to rhizobial infection, with much of the root non-responsive. To partially overcome this issue, we adopted translating ribosome affinity purification (TRAP) to specifically monitor the response of the root cortex to rhizobial inoculation using a cortex-specific promoter. While previous studies have largely focused on the plant response within the root epidermis (e.g., root hairs) or within developing nodules, much less is known about the early responses within the root cortex, such as in relation to the development of the nodule primordium or growth of the infection thread. We focused on identifying genes specifically regulated during early nodule organogenesis using roots inoculated with Bradyrhizobium japonicum. A number of novel nodulation gene candidates were discovered, as well as soybean orthologs of nodulation genes previously reported in other legumes. The differential cortex expression of several genes was confirmed using a promoter-GUS analysis, and RNAi was used to investigate gene function. Notably, a number of differentially regulated genes involved in phytohormone signaling, including auxin, cytokinin, and gibberellic acid (GA), were also discovered, providing deep insight into phytohormone signaling during early nodule development.
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Affiliation(s)
- Jae Hyo Song
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Bruna Montes-Luz
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Michelle Zibetti Tadra-Sfeir
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Yaya Cui
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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Teixeira RT, Fortes AM, Bai H, Pinheiro C, Pereira H. Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection. PLANTA 2018; 247:317-338. [PMID: 28988391 DOI: 10.1007/s00425-017-2786-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
The phenylpropanoid pathway impacts the cork quality development. In cork of bad quality, the flavonoid route is favored, whereas in good quality, cork lignin and suberin production prevails. Cork oaks develop a thick cork tissue as a protective shield that results of the continuous activity of a secondary meristem, the cork cambium, or phellogen. Most studies applied to developmental processes do not consider the cell types from which the samples were extracted. Here, laser microdissection (LM) coupled with transcript profiling using RNA sequencing (454 pyrosequencing) was applied to phellogen cells of trees producing low- and good quality cork. Functional annotation and functional enrichment analyses showed that stress-related genes are enriched in samples extracted from trees producing good quality cork (GQC). This process is under tight transcriptional (transcription factors, kinases) regulation and also hormonal control involving ABA, ethylene, and auxins. The phellogen cells collected from trees producing bad quality cork (BQC) show a consistent up-regulation of genes belonging to the flavonoid pathway as a response to stress. They also display a different modulation of cell wall genes resulting into a thinner cork layer, i.e., less meristematic activity. Based on the analysis of the phenylpropanoid pathway regulating genes, in GQC, the synthesis of lignin and suberin is promoted, whereas in BQC, the same pathway favors the biosynthesis of free phenolic compounds. This study provided new insights of how cell-specific gene expression can determine tissue and organ morphology and physiology and identified robust candidate genes that can be used in breeding programs aiming at improving cork quality.
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Affiliation(s)
- Rita Teresa Teixeira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute, State University, Blacksburg, VA, 24060, USA.
| | - Ana Margarida Fortes
- BIOISI, Science Faculty, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Hua Bai
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute, State University, Blacksburg, VA, 24060, USA
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Helena Pereira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
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Warnasooriya SN, Montgomery BL. Using transgenic modulation of protein synthesis and accumulation to probe protein signaling networks in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2011; 6:1312-21. [PMID: 21862868 PMCID: PMC3258059 DOI: 10.4161/psb.6.9.16437] [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] [Indexed: 05/04/2023]
Abstract
Deployment of new model species in the plant biology community requires the development and/or improvement of numerous genetic tools. Sequencing of the Arabidopsis thaliana genome opened up a new challenge of assigning biological function to each gene. As many genes exhibit spatiotemporal or other conditional regulation of biological processes, probing for gene function necessitates applications that can be geared toward temporal, spatial and quantitative functional analysis in vivo. The continuing quest to establish new platforms to examine plant gene function has resulted in the availability of numerous genomic and proteomic tools. Classical and more recent genome-wide experimental approaches include conventional mutagenesis, tagged DNA insertional mutagenesis, ectopic expression of transgenes, activation tagging, RNA interference and two-component transactivation systems. The utilization of these molecular tools has resulted in conclusive evidence for the existence of many genes, and expanded knowledge on gene structure and function. This review covers several molecular tools that have become increasingly useful in basic plant research. We discuss their advantages and limitations for probing cellular protein function while emphasizing the contributions made to lay the fundamental groundwork for genetic manipulation of crops using plant biotechnology.
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Affiliation(s)
- Sankalpi N Warnasooriya
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
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Schiebold S, Tschiersch H, Borisjuk L, Heinzel N, Radchuk R, Rolletschek H. A novel procedure for the quantitative analysis of metabolites, storage products and transcripts of laser microdissected seed tissues of Brassica napus. PLANT METHODS 2011; 7:19. [PMID: 21718489 PMCID: PMC3141804 DOI: 10.1186/1746-4811-7-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/30/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND The biology of the seed is complicated by the extensive non-homogeneity (spatial gradients) in gene expression, metabolic conversions and storage product accumulation. The detailed understanding of the mechanisms underlying seed growth and storage therefore requires the development of means to obtain tissue-specific analyses. This approach also represents an important priority in the context of seed biotechnology. RESULTS We provide a guideline and detailed procedures towards the quantitative analysis of laser micro-dissected (LM) tissues in oilseed rape (Brassica napus). This includes protocols for laser microdissection of the seed, and the subsequent extraction and quantitative analysis of lipids, starch and metabolites (sugars, sugar phosphates, nucleotides, amino acids, intermediates of glycolysis and citric acid cycle). We have also developed a protocol allowing the parallel analysis of the transcriptome using Brassica-specific microarrays. Some data are presented regarding the compartmentation of metabolites within the oilseed rape embryo. CONCLUSION The described methodology allows for the rapid, combined analysis of metabolic intermediates, major storage products and transcripts in a tissue-specific manner. The protocols are robust for oilseed rape, and should be readily adjustable for other crop species. The suite of methods applied to LM tissues represents an important step in the context of both the systems biology and the biotechnology of oilseeds.
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Affiliation(s)
- Silke Schiebold
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Ljudmilla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Nicolas Heinzel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Ruslana Radchuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
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Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Nagata T, Niihama M, Kato H, Kikuchi S, Hamada K, Mochizuki T, Ishimizu T, Iwai H, Tsutsumi N, Kurata N. Rice expression atlas in reproductive development. PLANT & CELL PHYSIOLOGY 2010; 51:2060-81. [PMID: 21062870 DOI: 10.1093/pcp/pcq165] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. A decrease in expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes which appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several cyclin-dependent kinases (CDKs), cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the most extensive and most comprehensive data set available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.
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Affiliation(s)
- Masahiro Fujita
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540 Japan
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Hacquard S, Delaruelle C, Legué V, Tisserant E, Kohler A, Frey P, Martin F, Duplessis S. Laser capture microdissection of uredinia formed by Melampsora larici-populina revealed a transcriptional switch between biotrophy and sporulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1275-86. [PMID: 20831407 DOI: 10.1094/mpmi-05-10-0111] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The foliar rust caused by the basidiomycete Melampsora larici-populina is the main disease affecting poplar plantations in Europe. The biotrophic status of rust fungi is a major limitation to study gene expression of cell or tissue types during host infection. At the uredinial stage, infected poplar leaves contain distinct rust tissues such as haustoria, infection hyphae, and uredinia with sporogenous hyphae and newly formed asexual urediniospores. Laser capture microdissection (LCM) was used to isolate three areas corresponding to uredinia and subjacent zones in the host mesophyll for expression analysis with M. larici-populina whole-genome exon oligoarrays. Optimization of tissue preparation prior to LCM allowed isolation of RNA of good integrity for genome-wide expression profiling. Our results indicate that the poplar rust uredinial stage is marked by distinct genetic programs related to biotrophy in the host palisade mesophyll and to sporulation in the uredinium. A strong induction of transcripts encoding small secreted proteins, likely containing rust effectors, is observed in the mesophyll, suggesting a late maintenance of suppression of host defense in the tissue containing haustoria and infection hyphae. On the other hand, cell cycle and cell defense rescue transcripts are strongly accumulated in the sporulation area. This combined LCM-transcriptomic approach brings new insights on the molecular mechanisms underlying urediniospore formation in rust fungi.
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Affiliation(s)
- Stéphane Hacquard
- Unité Mixte de Recherche 1136 INRA/Nancy Université Interactions Arbres/Micro-organismes, Champenoux, France
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Gomez SK, Harrison MJ. Laser microdissection and its application to analyze gene expression in arbuscular mycorrhizal symbiosis. PEST MANAGEMENT SCIENCE 2009; 65:504-511. [PMID: 19206091 DOI: 10.1002/ps.1715] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phosphorus is essential for plant growth, and in many soils phosphorus availability limits crop production. Most plants in natural ecosystems obtain phosphorus via a symbiotic partnership with arbuscular mycorrhizal (AM) fungi. While the significance of these associations is apparent, their molecular basis is poorly understood. Consequently, the potential to harness the mycorrhizal symbiosis to improve phosphorus nutrition in agriculture is not realized. Transcript profiling has recently been used to investigate gene expression changes that accompany development of the AM symbiosis. While these approaches have enabled the identification of AM-symbiosis-associated genes, they have generally involved the use of RNA from whole mycorrhizal roots. Laser microdissection techniques allow the dissection and capture of individual cells from a tissue. RNA can then be isolated from these samples and cell-type specific gene expression information can be obtained. This technology has been applied to obtain cells from plants and more recently to study plant-microbe interactions. The latter techniques, particularly those developed for root-microbe interactions, are of relevance to plant-parasitic weed research. Here, laser microdissection, its use in plant biology and in particular plant-microbe interactions are discussed. An overview of the AM symbiosis is then provided, with a focus on recent advances in understanding development of the arbuscule-cortical cell interface. Finally, the recent applications of laser microdissection for analyses of AM symbiosis are discussed.
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Affiliation(s)
- S Karen Gomez
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY 14850, USA
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Nelson T, Gandotra N, Tausta SL. Plant cell types: reporting and sampling with new technologies. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:567-73. [PMID: 18653377 DOI: 10.1016/j.pbi.2008.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/12/2008] [Accepted: 06/12/2008] [Indexed: 05/21/2023]
Abstract
Plants have relatively few cell types, but their specialized functions and their interactions are essential for physiology, development, and defense. The contributions of individual cells have been distinguished by methods including in situ reporting, cell sampling, and cell separation, thus far mostly limited to measurement of single transcripts, proteins, or metabolites. Advances in transcriptomics, proteomics, metabolomics, and activity assays with small samples and in the modeling of these data into networks of expression, regulation, interaction, and metabolism make it possible to evaluate the roles of cell types at system levels. Recent analyses include cell types of developing roots, bundle sheath and mesophyll cells of C4-type leaves, xylem and phloem cells of vascular systems, and specialized regions of embryos and shoot apices.
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Affiliation(s)
- Timothy Nelson
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208104, New Haven, CT 06520-8104, USA.
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