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Trösch R, Jarvis P. The stromal processing peptidase of chloroplasts is essential in Arabidopsis, with knockout mutations causing embryo arrest after the 16-cell stage. PLoS One 2011; 6:e23039. [PMID: 21857988 PMCID: PMC3156710 DOI: 10.1371/journal.pone.0023039] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/05/2011] [Indexed: 11/19/2022] Open
Abstract
Stromal processing peptidase (SPP) is a metalloendopeptidase located in the stroma of chloroplasts, and it is responsible for the cleavage of transit peptides from preproteins upon their import into the organelle. Two independent mutant Arabidopsis lines with T-DNA insertions in the SPP gene were analysed (spp-1 and spp-2). For both lines, no homozygous mutant plants could be detected, and the segregating progeny of spp heterozygotes contained heterozygous and wild-type plants in a ratio of 2∶1. The siliques of heterozygous spp-1 and spp-2 plants contained many aborted seeds, at a frequency of ∼25%, suggesting embryo lethality. By contrast, transmission of the spp mutations through the male and female gametes was found to be normal, and so gametophytic effects could be ruled out. To further elucidate the timing of the developmental arrest, mutant and wild-type seeds were cleared and analysed by Nomarski microscopy. A significant proportion (∼25%) of the seeds in mutant siliques exhibited delayed embryogenesis compared to those in wild type. Moreover, the mutant embryos never progressed normally beyond the 16-cell stage, with cell divisions not completing properly thereafter. Heterozygous spp mutant plants were phenotypically indistinguishable from the wild type, indicating that the spp knockout mutations are completely recessive and suggesting that one copy of the SPP gene is able to produce sufficient SPP protein for normal development under standard growth conditions.
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Affiliation(s)
- Raphael Trösch
- Department of Biology, University of Leicester, Leicester, United Kingdom
| | - Paul Jarvis
- Department of Biology, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Guan X, Lee JJ, Pang M, Shi X, Stelly DM, Chen ZJ. Activation of Arabidopsis seed hair development by cotton fiber-related genes. PLoS One 2011; 6:e21301. [PMID: 21779324 PMCID: PMC3136922 DOI: 10.1371/journal.pone.0021301] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/25/2011] [Indexed: 02/07/2023] Open
Abstract
Each cotton fiber is a single-celled seed trichome or hair, and over 20,000 fibers may develop semi-synchronously on each seed. The molecular basis for seed hair development is unknown but is likely to share many similarities with leaf trichome development in Arabidopsis. Leaf trichome initiation in Arabidopsis thaliana is activated by GLABROUS1 (GL1) that is negatively regulated by TRIPTYCHON (TRY). Using laser capture microdissection and microarray analysis, we found that many putative MYB transcription factor and structural protein genes were differentially expressed in fiber and non-fiber tissues. Gossypium hirsutum MYB2 (GhMYB2), a putative GL1 homolog, and its downstream gene, GhRDL1, were highly expressed during fiber cell initiation. GhRDL1, a fiber-related gene with unknown function, was predominately localized around cell walls in stems, sepals, seed coats, and pollen grains. GFP:GhRDL1 and GhMYB2:YFP were co-localized in the nuclei of ectopic trichomes in siliques. Overexpressing GhRDL1 or GhMYB2 in A. thaliana Columbia-0 (Col-0) activated fiber-like hair production in 4–6% of seeds and had on obvious effects on trichome development in leaves or siliques. Co-overexpressing GhRDL1 and GhMYB2 in A. thaliana Col-0 plants increased hair formation in ∼8% of seeds. Overexpressing both GhRDL1 and GhMYB2 in A. thaliana Col-0 try mutant plants produced seed hair in ∼10% of seeds as well as dense trichomes inside and outside siliques, suggesting synergistic effects of GhRDL1 and GhMYB2 with try on development of trichomes inside and outside of siliques and seed hair in A. thaliana. These data suggest that a different combination of factors is required for the full development of trichomes (hairs) in leaves, siliques, and seeds. A. thaliana can be developed as a model a system for discovering additional genes that control seed hair development in general and cotton fiber in particular.
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Affiliation(s)
- Xueying Guan
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jinsuk J. Lee
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Mingxiong Pang
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Xiaoli Shi
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - David M. Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Z. Jeffrey Chen
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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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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54
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Xiang D, Venglat P, Tibiche C, Yang H, Risseeuw E, Cao Y, Babic V, Cloutier M, Keller W, Wang E, Selvaraj G, Datla R. Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis. PLANT PHYSIOLOGY 2011; 156:346-56. [PMID: 21402797 PMCID: PMC3091058 DOI: 10.1104/pp.110.171702] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/11/2010] [Indexed: 05/18/2023]
Abstract
Embryogenesis is central to the life cycle of most plant species. Despite its importance, because of the difficulty associated with embryo isolation, global gene expression programs involved in plant embryogenesis, especially the early events following fertilization, are largely unknown. To address this gap, we have developed methods to isolate whole live Arabidopsis (Arabidopsis thaliana) embryos as young as zygote and performed genome-wide profiling of gene expression. These studies revealed insights into patterns of gene expression relating to: maternal and paternal contributions to zygote development, chromosomal level clustering of temporal expression in embryogenesis, and embryo-specific functions. Functional analysis of some of the modulated transcription factor encoding genes from our data sets confirmed that they are critical for embryogenesis. Furthermore, we constructed stage-specific metabolic networks mapped with differentially regulated genes by combining the microarray data with the available Kyoto Encyclopedia of Genes and Genomes metabolic data sets. Comparative analysis of these networks revealed the network-associated structural and topological features, pathway interactions, and gene expression with reference to the metabolic activities during embryogenesis. Together, these studies have generated comprehensive gene expression data sets for embryo development in Arabidopsis and may serve as an important foundational resource for other seed plants.
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Bi YP, Liu W, Xia H, Su L, Zhao CZ, Wan SB, Wang XJ. EST sequencing and gene expression profiling of cultivated peanut (Arachis hypogaea L.). Genome 2011; 53:832-9. [PMID: 20962890 DOI: 10.1139/g10-074] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peanut (Arachis hypogaea L.) is one of the most important oil crops in the world. However, biotechnological based improvement of peanut is far behind many other crops. It is critical and urgent to establish the biotechnological platform for peanut germplasm innovation. In this study, a peanut seed cDNA library was constructed to establish the biotechnological platform for peanut germplasm innovation. About 17,000 expressed sequence tags (ESTs) were sequenced and used for further investigation. Among which, 12.5% were annotated as metabolic related and 4.6% encoded transcription or post-transcription factors. ESTs encoding storage protein and enzymes related to protein degradation accounted for 28.8% and formed the largest group of the annotated ESTs. ESTs that encoded stress responsive proteins and pathogen-related proteins accounted for 5.6%. ESTs that encoded unknown proteins or showed no hit in the GenBank nr database accounted for 20.1% and 13.9%, respectively. A total number of 5066 EST sequences were selected to make a cDNA microarray. Expression analysis revealed that these sequences showed diverse expression patterns in peanut seeds, leaves, stems, roots, flowers, and gynophores. We also analyzed the gene expression pattern during seed development. Genes that were upregulated (≥twofold) at 15, 25, 35, and 45 days after pegging (DAP) were found and compared with 70 DAP. The potential value of these genes and their promoters in the peanut gene engineering study is discussed.
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Affiliation(s)
- Yu-Ping Bi
- High-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong, People's Republic of China
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56
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Suwabe K, Suzuki G, Watanabe M. Achievement of genetics in plant reproduction research: the past decade for the coming decade. Genes Genet Syst 2011; 85:297-310. [PMID: 21317542 DOI: 10.1266/ggs.85.297] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the last decade, a variety of innovations of emerging technologies in science have been accomplished. Advanced research environment in plant science has made it possible to obtain whole genome sequence in plant species. But now we recognize this by itself is not sufficient to understand the overall biological significance. Since Gregor Mendel established a principle of genetics, known as Mendel's Laws of Inheritance, genetics plays a prominent role in life science, and this aspect is indispensable even in modern plant biology. In this review, we focus on achievements of genetics on plant sexual reproduction research in the last decade and discuss the role of genetics for the coming decade. It is our hope that this will shed light on the importance of genetics in plant biology and provide valuable information to plant biologists.
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Affiliation(s)
- Keita Suwabe
- Graduate School of Bioresources, Mie University, Tsu, Japan
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57
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Techniques of cell type-specific transcriptome analysis and applications in researches of sexual plant reproduction. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11515-011-1090-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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58
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Abstract
Obligate plant-parasitic nematodes, such as cyst nematodes (Heterodera and Globodera spp.) and root-knot nematodes (Meloidogyne spp.), form specialized feeding cells in host plant roots. These feeding cells provide the sole source of nutrition for the growth and reproduction of the nematode to complete its life cycle. Feeding cell formation involves complex physiological and morphological changes to normal root cells and is accompanied by dramatic changes in plant gene expression. The distinct features of feeding cells suggest that their formation entails a unique gene expression profile, a better understanding of which will assist in building models to explain signaling pathways that modulate transcriptional changes in response to nematodes. Ultimately, this knowledge can be used to design strategies to develop resistance against nematodes in crop plants. Feeding cells comprise a small fraction of the total root cell population, and identification of plant gene expression changes specific to these cells is difficult. Until recently, the specific isolation of nematode feeding cells could be accomplished only by manual dissection or microaspiration. These approaches are limited in that only mature feeding cells can be isolated. These limitations in tissue accessibility for macromolecule isolation at different stages of feeding cell development can be overcome through the use of laser microdissection (LM), a technique that enables the specific isolation of feeding cells from early to late stages for RNA isolation, amplification, and downstream analysis.
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Affiliation(s)
- Nagabhushana Ithal
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
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59
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Chen C, Farmer AD, Langley RJ, Mudge J, Crow JA, May GD, Huntley J, Smith AG, Retzel EF. Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes. BMC PLANT BIOLOGY 2010; 10:280. [PMID: 21167045 PMCID: PMC3018465 DOI: 10.1186/1471-2229-10-280] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/17/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., Saccharomyces cerevisiae and Drosophila melanogaster), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes. RESULTS A high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes. CONCLUSION These findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.
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Affiliation(s)
- Changbin Chen
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN 55108, USA
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - Raymond J Langley
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
- Immunology, Lovelace Respiratory Research Institute, 2425 Ridgecrest Drive SE, Albuquerque, NM 87108, USA
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - John A Crow
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - Gregory D May
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - James Huntley
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
- Illumina Inc., Hayward, California 94545, USA
| | - Alan G Smith
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN 55108, USA
| | - Ernest F Retzel
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
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60
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Xin H, Sun M. What we have learned from transcript profile analyses of male and female gametes in flowering plants. SCIENCE CHINA-LIFE SCIENCES 2010; 53:927-33. [PMID: 20821291 DOI: 10.1007/s11427-010-4033-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 06/21/2010] [Indexed: 11/30/2022]
Abstract
Double fertilization is one of the predominant features of sexual reproduction in flowering plants but, because of the physical inaccessibility of gametes, the essential molecular mechanisms in these processes are largely unknown. Based on the techniques for isolating highly purified gametes from several species and well-developed methods for manipulating RNA from limited quantities of gametes, genome-wide investigations of gamete transcription profiles were recently conducted in flowering plants. In this review, we survey the accumulated knowledge on gamete collection and purification, cDNA library construction, and transcript profile analysis to assess our understanding of the molecular mechanisms of gamete specialization and fertilization.
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Affiliation(s)
- HaiPing Xin
- Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, China
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61
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Tebbji F, Nantel A, Matton DP. Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7 K cDNA microarray from Solanum chacoense ovules. BMC PLANT BIOLOGY 2010; 10:174. [PMID: 20704744 PMCID: PMC3095305 DOI: 10.1186/1471-2229-10-174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 08/12/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses. RESULTS We analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (>or= +/- 2 fold change, p value <or= 0.01) in fertilized ovules compared to unfertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with the vast majority of the fertilization-regulated genes specifically or predominantly expressed in ovules (955 genes). During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development. CONCLUSION Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time point allowed the identification of a subset of stage-specific and transition-specific genes.
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Affiliation(s)
- Faiza Tebbji
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, Québec, H1X 2B2, Canada
- Biotechnology Research Institute, National Research Council, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - André Nantel
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, Québec, H1X 2B2, Canada
- Biotechnology Research Institute, National Research Council, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Daniel P Matton
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, Québec, H1X 2B2, Canada
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Hu TX, Yu M, Zhao J. Comparative transcriptional profiling analysis of the two daughter cells from tobacco zygote reveals the transcriptome differences in the apical and basal cells. BMC PLANT BIOLOGY 2010; 10:167. [PMID: 20699003 PMCID: PMC3095300 DOI: 10.1186/1471-2229-10-167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 08/11/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND In angiosperm, after the first asymmetric zygotic cell division, the apical and basal daughter cells follow distinct development pathways. Global transcriptome analysis of these two cells is essential in understanding their developmental differences. However, because of the difficulty to isolate the in vivo apical and basal cells of two-celled proembryo from ovule and ovary in higher plants, the transcriptome analysis of them hasn't been reported. RESULTS In this study, we developed a procedure for isolating the in vivo apical and basal cells of the two-celled proembryo from tobacco (Nicotiana tabacum), and then performed a comparative transcriptome analysis of the two cells by suppression subtractive hybridization (SSH) combined with macroarray screening. After sequencing, we identified 797 differentially expressed ESTs corresponding to 299 unigenes. Library sequence analysis successfully identified tobacco homologies of genes involved in embryogenesis and seed development. By quantitative real-time PCR, we validated the differential expression of 40 genes, with 6 transcripts of them specifically expressed in the apical or basal cell. Expression analysis also revealed some transcripts displayed cell specific activation in one of the daughter cells after zygote division. These differential expressions were further validated by in situ hybridization (ISH). Tissue expression pattern analysis also revealed some potential roles of these candidate genes in development. CONCLUSIONS The results show that some differential or specific transcripts in the apical and basal cells of two-celled proembryo were successfully isolated, and the identification of these transcripts reveals that these two daughter cells possess distinct transcriptional profiles after zygote division. Further functional work on these differentially or specifically expressed genes will promote the elucidation of molecular mechanism controlling early embryogenesis.
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Affiliation(s)
- Tian-Xiang Hu
- Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Miao Yu
- Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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63
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van den Burg HA, Kini RK, Schuurink RC, Takken FLW. Arabidopsis small ubiquitin-like modifier paralogs have distinct functions in development and defense. THE PLANT CELL 2010; 22:1998-2016. [PMID: 20525853 PMCID: PMC2910984 DOI: 10.1105/tpc.109.070961] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 04/28/2010] [Accepted: 05/13/2010] [Indexed: 05/20/2023]
Abstract
Posttranslational modifications allow dynamic and reversible changes to protein function. In Arabidopsis thaliana, a small gene family encodes paralogs of the small ubiquitin-like posttranslational modifier. We studied the function of these paralogs. Single mutants of the SUM1 and SUM2 paralogs do not exhibit a clear phenotype. However, the corresponding double knockdown mutant revealed that SUM1 and SUM2 are essential for plant development, floral transition, and suppression of salicylic acid (SA)-dependent defense responses. The SUM1 and SUM2 genes are constitutively expressed, but their spatial expression patterns do not overlap. Tight transcriptional regulation of these two SUM genes appears to be important, as overexpression of either wild-type or conjugation-deficient mutants resulted in activation of SA-dependent defense responses, as did the sum1 sum2 knockdown mutant. Interestingly, expression of the paralog SUM3 is strongly and widely induced by SA and by the defense elicitor Flg22, whereas its expression is otherwise low and restricted to a few specific cell types. Loss of SUM3 does not result in an aberrant developmental phenotype except for late flowering, while SUM3 overexpression causes early flowering and activates plant defense. Apparently, SUM3 promotes plant defense downstream of SA, while SUM1 and SUM2 together prevent SA accumulation in noninfected plants.
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Affiliation(s)
- Harrold A van den Burg
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
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Holman TJ, Wilson MH, Kenobi K, Dryden IL, Hodgman TC, Wood ATA, Holdsworth MJ. Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray. PLANT METHODS 2010; 6:9. [PMID: 20230623 PMCID: PMC2847557 DOI: 10.1186/1746-4811-6-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 03/15/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microarrays are a powerful tool used for the determination of global RNA expression. There is an increasing requirement to focus on profiling gene expression in tissues where it is difficult to obtain large quantities of material, for example individual tissues within organs such as the root, or individual isolated cells. From such samples, it is difficult to produce the amount of RNA required for labelling and hybridisation in microarray experiments, thus a process of amplification is usually adopted. Despite the increasing use of two-cycle amplification for transcriptomic analyses on the Affymetrix ATH1 array, there has been no report investigating any potential bias in gene representation that may occur as a result. RESULTS Here we compare transcriptomic data generated using Affymetrix one-cycle (standard labelling protocol), two-cycle (small-sample protocol) and IVT-Express protocols with the Affymetrix ATH1 array using Arabidopsis root samples. Results obtained with each protocol are broadly similar. However, we show that there are 35 probe sets (of a total of 22810) that are misrepresented in the two-cycle data sets. Of these, 33 probe sets were classed as mis-amplified when comparisons of two independent publicly available data sets were undertaken. CONCLUSIONS Given the unreliable nature of the highlighted probes, we caution against using data associated with the corresponding genes in analyses involving transcriptomic data generated with two-cycle amplification protocols. We have shown that the Affymetrix IVT-E labelling protocol produces data with less associated bias than the two-cycle protocol, and as such, would recommend this kit for new experiments that involve small samples.
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Affiliation(s)
- Tara J Holman
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Michael H Wilson
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Kim Kenobi
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Ian L Dryden
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - T Charlie Hodgman
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Andrew TA Wood
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael J Holdsworth
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
- Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
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65
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Wuest SE, Vijverberg K, Schmidt A, Weiss M, Gheyselinck J, Lohr M, Wellmer F, Rahnenführer J, von Mering C, Grossniklaus U. Arabidopsis Female Gametophyte Gene Expression Map Reveals Similarities between Plant and Animal Gametes. Curr Biol 2010; 20:506-12. [DOI: 10.1016/j.cub.2010.01.051] [Citation(s) in RCA: 218] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 01/08/2010] [Accepted: 01/12/2010] [Indexed: 10/19/2022]
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66
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De Smet I, Lau S, Mayer U, Jürgens G. Embryogenesis - the humble beginnings of plant life. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:959-70. [PMID: 20409270 DOI: 10.1111/j.1365-313x.2010.04143.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Each plant starts life from the zygote formed by the fusion of an egg and a sperm cell. The zygote gives rise to a multicellular embryo that displays a basic plant body organization and is surrounded by nutritive endosperm and maternal tissue. How the body organization is generated had already been studied before the genome sequence of Arabidopsis thaliana was completed 10 years ago, but several regulatory mechanisms of embryo development have since been discovered or analysed in more detail. Although this progress did not strictly depend on the availability of the genome sequence itself, several advances were considerably facilitated. In this review, we mainly address early embryo development, highlighting general mechanisms and crucial regulators, including phytohormones, that are involved in patterning the embryo and were mainly analysed in the post-genome decade. We also highlight some unsolved problems, provide a brief outlook on the future of Arabidopsis embryo research, and discuss how the knowledge gained from Arabidopsis could be translated to crop species.
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Affiliation(s)
- Ive De Smet
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 3, Tübingen, Germany
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67
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Yang X, Zhang X. Regulation of Somatic Embryogenesis in Higher Plants. CRITICAL REVIEWS IN PLANT SCIENCES 2010; 29:36-57. [PMID: 0 DOI: 10.1080/07352680903436291] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Xiyan Yang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
| | - Xianlong Zhang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
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68
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Abstract
High-resolution cellular analysis will help answer many important questions in plant biology including how genetic information is differentially used to enable the formation and development of the plant body. By comparing transcriptome data from distinct cell types during various stages of development, insight can be obtained into the transcriptional networks that underpin the attributes and contributions of particular cells and tissues. Laser microdissection (LM) is a technique that enables researchers to obtain specific cells or tissues from histological samples in a manner conducive to downstream molecular analysis. LM has become an established strategy in many areas of biology and it has recently been adapted for use with many types of plant tissue.
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Affiliation(s)
- Robert C Day
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
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69
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Karami O, Aghavaisi B, Mahmoudi Pour A. Molecular aspects of somatic-to-embryogenic transition in plants. J Chem Biol 2009; 2:177-90. [PMID: 19763658 PMCID: PMC2763145 DOI: 10.1007/s12154-009-0028-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Revised: 08/18/2009] [Accepted: 08/25/2009] [Indexed: 11/30/2022] Open
Abstract
Somatic embryogenesis (SE) is a model system for understanding the physiological, biochemical, and molecular biological events occurring during plant embryo development. Plant somatic cells have the ability to undergo sustained divisions and give rise to an entire organism. This remarkable feature is called plant cell totipotency. SE is a notable illustration of plant totipotency and involves reprogramming of development in somatic cells toward the embryogenic pathway. Plant growth regularities, especially auxins, are key components as their exogenous application recapitulates the embryogenic potential of the mitotically quiescent somatic cells. It has been observed that there are genetic and also physiological factors that trigger in vitro embryogenesis in various types of plant somatic cells. Analysis of the proteome and transcriptome has led to the identification and characterization of certain genes involved in SE. Most of these genes, however, are upregulated only in the late developmental stages, suggesting that they do not play a direct role in the vegetative-to-embryogenic transition. However, the molecular bases of those triggering factors and the genetic and biochemical mechanisms leading to in vitro embryogenesis are still unknown. Here, we describe the plant factors that participate in the vegetative-to-embryogenic transition and discuss their possible roles in this process.
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Affiliation(s)
- Omid Karami
- Department of Biotechnology, Bu-Ali Sina University, Hamedan, Iran
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70
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Agustí J, Merelo P, Cercós M, Tadeo FR, Talón M. Comparative transcriptional survey between laser-microdissected cells from laminar abscission zone and petiolar cortical tissue during ethylene-promoted abscission in citrus leaves. BMC PLANT BIOLOGY 2009; 9:127. [PMID: 19852773 PMCID: PMC2770498 DOI: 10.1186/1471-2229-9-127] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 10/23/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Abscission is the cell separation process by which plants are able to shed organs. It has a great impact on the yield of most crop plants. At the same time, the process itself also constitutes an excellent model to study cell separation processes, since it occurs in concrete areas known as abscission zones (AZs) which are composed of a specific cell type. However, molecular approaches are generally hampered by the limited area and cell number constituting the AZ. Therefore, detailed studies at the resolution of cell type are of great relevance in order to accurately describe the process and to identify potential candidate genes for biotechnological applications. RESULTS Efficient protocols for the isolation of specific citrus cell types, namely laminar abscission zone (LAZ) and petiolar cortical (Pet) cells based on laser capture microdissection (LCM) and for RNA microextraction and amplification have been developed. A comparative transcriptome analysis between LAZ and Pet from citrus leaf explants subjected to an in-vitro 24 h ethylene treatment was performed utilising microarray hybridization and analysis. Our analyses of gene functional classes differentially represented in ethylene-treated LAZ revealed an activation program dominated by the expression of genes associated with protein synthesis, protein fate, cell type differentiation, development and transcription. The extensive repertoire of genes associated with cell wall biosynthesis and metabolism strongly suggests that LAZ layers activate both catabolic and anabolic wall modification pathways during the abscission program. In addition, over-representation of particular members of different transcription factor families suggests important roles for these genes in the differentiation of the effective cell separation layer within the many layers contained in the citrus LAZ. Preferential expression of stress-related and defensive genes in Pet reveals that this tissue is likely to be reprogrammed to prevent pathogen attacks and general abiotic stresses after organ shedding. CONCLUSION The LCM-based data generated in this survey represent the most accurate description of the main biological processes and genes involved in organ abscission in citrus. This study provides novel molecular insight into ethylene-promoted leaf abscission and identifies new putative target genes for characterization and manipulation of organ abscission in citrus.
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Affiliation(s)
- Javier Agustí
- Instituto Valenciano de Investigaciones Agrarias - Centro de Genómica. Carretera Moncada-Náquera Km. 4,5. 46113 Moncada (Valencia) Spain
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Paz Merelo
- Instituto Valenciano de Investigaciones Agrarias - Centro de Genómica. Carretera Moncada-Náquera Km. 4,5. 46113 Moncada (Valencia) Spain
| | - Manuel Cercós
- Instituto Valenciano de Investigaciones Agrarias - Centro de Genómica. Carretera Moncada-Náquera Km. 4,5. 46113 Moncada (Valencia) Spain
| | - Francisco R Tadeo
- Instituto Valenciano de Investigaciones Agrarias - Centro de Genómica. Carretera Moncada-Náquera Km. 4,5. 46113 Moncada (Valencia) Spain
| | - Manuel Talón
- Instituto Valenciano de Investigaciones Agrarias - Centro de Genómica. Carretera Moncada-Náquera Km. 4,5. 46113 Moncada (Valencia) Spain
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71
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Scanlon MJ, Ohtsu K, Timmermans MCP, Schnable PS. Laser microdissection-mediated isolation and in vitro transcriptional amplification of plant RNA. ACTA ACUST UNITED AC 2009; Chapter 25:Unit 25A.3. [PMID: 19575479 DOI: 10.1002/0471142727.mb25a03s87] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protocols for laser microdissection and linear amplification of RNA from fixed, sectioned plant tissues are described. When combined with quantitative RT-PCR, microarray analysis, or RNA-sequencing, these procedures enable quantitative analyses of transcript accumulation from microscopic quantities of specific plant organs, tissues, or single cells.
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72
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Zhang H, Ogas J. An epigenetic perspective on developmental regulation of seed genes. MOLECULAR PLANT 2009; 2:610-627. [PMID: 19825643 DOI: 10.1093/mp/ssp027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The developmental program of seeds is promoted by master regulators that are expressed in a seed-specific manner. Ectopic expression studies reveal that expression of these master regulators and other transcriptional regulators is sufficient to promote seed-associated traits, including generation of somatic embryos. Recent work highlights the importance of chromatin-associated factors in restricting expression of seed-specific genes, in particular PcG proteins and ATP-dependent remodelers. This review summarizes what is known regarding factors that promote zygotic and/or somatic embryogenesis and the chromatin machinery that represses their expression. Characterization of the regulation of seed-specific genes reveals that plant chromatin-based repression systems exhibit broad conservation with and surprising differences from animal repression systems.
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Affiliation(s)
- Heng Zhang
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA.
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73
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Portillo M, Lindsey K, Casson S, García-Casado G, Solano R, Fenoll C, Escobar C. Isolation of RNA from laser-capture-microdissected giant cells at early differentiation stages suitable for differential transcriptome analysis. MOLECULAR PLANT PATHOLOGY 2009; 10:523-35. [PMID: 19523105 PMCID: PMC6640446 DOI: 10.1111/j.1364-3703.2009.00552.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant organ gene expression profile analyses are complicated by the various cell types, and therefore transcription patterns, present in each organ. For example, each gall formed in roots following root knot nematode infection contains between four and eight specialized feeding cells (giant cells, GCs) embedded within hypertrophied root tissues. A recent goal in plant science has been the isolation of nematode feeding cell mRNAs for subsequent gene expression analysis. By adapting current protocols for different plant species and cells, we have developed a simple and rapid method for obtaining GCs from frozen tissue sections of tomato with good morphology and preserved RNA. The tissue sections obtained were suitable for the laser capture microdissection of GCs 6-7 days post-infection, and even of very early developing GCs (48-72 h post-infection), by fixation of tissue with ethanol-acetic acid, infiltration with sucrose and freezing in isopentane with optimal cutting temperature medium. This process was also successful for obtaining control vascular cells from uninfected roots for direct comparison with GCs. A minimum of about 300 GCs and 600 control vascular cells was required for efficient linear RNA amplification through in vitro transcription. Laser capture microdissection-derived RNA, after two rounds of amplification, was successfully used for microarray hybridization and validated with several differentially expressed genes by quantitative polymerase chain reaction. Consistent with our results, 117 homologous genes were found to be co-regulated in a previous microarray analysis of Arabidopsis galls at the same developmental stage. Therefore, we conclude that our method allows the isolation of a sufficient quantity of RNA with a high quality/integrity, appropriate for differential transcriptome analysis.
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74
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Brooks L, Strable J, Zhang X, Ohtsu K, Zhou R, Sarkar A, Hargreaves S, Elshire RJ, Eudy D, Pawlowska T, Ware D, Janick-Buckner D, Buckner B, Timmermans MCP, Schnable PS, Nettleton D, Scanlon MJ. Microdissection of shoot meristem functional domains. PLoS Genet 2009; 5:e1000476. [PMID: 19424435 PMCID: PMC2673047 DOI: 10.1371/journal.pgen.1000476] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 04/09/2009] [Indexed: 12/30/2022] Open
Abstract
The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection-microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes that function during leaf development. Nine hundred and sixty-two differentially expressed maize genes were detected; control genes known to be upregulated in the initiating leaf (P0/P1) or in the SAM proper verified the precision of the microdissections. Genes involved in cell division/growth, cell wall biosynthesis, chromatin remodeling, RNA binding, and translation are especially upregulated in initiating leaves, whereas genes functioning during protein fate and DNA repair are more abundant in the SAM proper. In situ hybridization analyses confirmed the expression patterns of six previously uncharacterized maize genes upregulated in the P0/P1. P0/P1-upregulated genes that were also shown to be downregulated in leaf-arrested shoots treated with an auxin transport inhibitor are especially implicated to function during early events in maize leaf initiation. Reverse genetic analyses of asceapen1 (asc1), a maize D4-cyclin gene upregulated in the P0/P1, revealed novel leaf phenotypes, less genetic redundancy, and expanded D4-CYCLIN function during maize shoot development as compared to Arabidopsis. These analyses generated a unique SAM domain-specific database that provides new insight into SAM function and a useful platform for reverse genetic analyses of shoot development in maize.
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Affiliation(s)
- Lionel Brooks
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Josh Strable
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Xiaolan Zhang
- Plant Biology Department, University of Georgia, Athens, Georgia, United States of America
| | - Kazuhiro Ohtsu
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Ruilian Zhou
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Ananda Sarkar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Sarah Hargreaves
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Robert J. Elshire
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Douglas Eudy
- Division of Science, Truman State University, Kirksville, Missouri, United States of America
| | - Teresa Pawlowska
- Department of Plant Pathology, Ithaca, New York, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Agriculture Research Service Department, United States Department of Agriculture, Washington, D.C., United States of America
| | - Diane Janick-Buckner
- Division of Science, Truman State University, Kirksville, Missouri, United States of America
| | - Brent Buckner
- Division of Science, Truman State University, Kirksville, Missouri, United States of America
| | | | - Patrick S. Schnable
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Michael J. Scanlon
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
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75
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Mizumoto K, Hatano H, Hirabayashi C, Murai K, Takumi S. Altered expression of wheat AINTEGUMENTA homolog, WANT-1, in pistil and pistil-like transformed stamen of an alloplasmic line with Aegilops crassa cytoplasm. Dev Genes Evol 2009; 219:175-87. [PMID: 19255779 DOI: 10.1007/s00427-009-0275-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
Abstract
Homeotic transformation of stamens into pistil-like structures, called pistillody, has been reported in some alloplasmic common wheat lines with Aegilops crassa cytoplasm. An alloplasmic line of Chinese Spring ditelosomic 7BS (CSdt7BS) with Ae. crassa cytoplasm lacking the long arm of the chromosome 7B shows pistillody, and the pistils and transformed stamens are sterile due to abnormal ovule development. To elucidate the molecular mechanism of the ovule abnormality, we compared the expression profiles of floral organs between euplasmic and alloplasmic CSdt7BS lines. Two differential display methods of mRNA profiling demonstrated that Ae. crassa cytoplasm largely affects nuclear gene expression profiles of common wheat. Of the differentially expressed genes, a wheat AINTEGUMENTA (ANT) homolog, WANT-1, was preferentially expressed in pistils but not in stamens, and accumulation of the transcript was limited to ovule primordia at the floral organ development stage. In alloplasmic wheat, WANT-1 expression was patchy and weak at the ovule-development stages. On the other hand, no significant difference in gene expression patterns of wheat AGAMOUS (AG) homologs (WAG-1 and WAG-2) was observed between fertile and sterile pistils. These results indicated that alteration of gene expression after initiation of ovule primordia results in abnormal ovule development, and that the aberrant ovule formation is at least partly associated with the weak expression of WANT-1 around ovule primordia in alloplasmic wheat with Ae. crassa cytoplasm.
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Affiliation(s)
- Kota Mizumoto
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
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76
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Izumi Y, Kajiyama S, Nakamura R, Ishihara A, Okazawa A, Fukusaki E, Kanematsu Y, Kobayashi A. High-resolution spatial and temporal analysis of phytoalexin production in oats. PLANTA 2009; 229:931-943. [PMID: 19148672 DOI: 10.1007/s00425-008-0887-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 12/23/2008] [Indexed: 05/27/2023]
Abstract
The production of oat (Avena sativa L.) phytoalexins, avenanthramides, occurs in response to elicitor treatment with oligo-N-acetylchitooligosaccharides. In this study, avenanthramides production was investigated by techniques that provide high spatial and temporal resolution in order to clarify the process of phytoalexin production at the cellular level. The amount of avenanthramides accumulation in a single mesophyll cell was quantified by a combination of laser micro-sampling and low-diffuse nanoflow liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) techniques. Avenanthramides, NAD(P)H and chlorophyll were also visualized in elicitor-treated mesophyll cells using line-scanning fluorescence microscopy. We found that elicitor-treated mesophyll cells could be categorized into three characteristic cell phases, which occurred serially over time. Phase 0 indicated the normal cell state before metabolic or morphological change in response to elicitor, in which the cells contained abundant NAD(P)H. In phase 1, rapid NAD(P)H oxidation and marked movement of chloroplasts occurred, and this phase was the early stage of avenanthramides biosynthesis. In phase 2, avenanthramides accumulation was maximized, and chloroplasts were degraded. Avenanthramides appear to be synthesized in the chloroplast, because a fluorescence signal originating from avenanthramides was localized to the chloroplasts. Moreover, our results indicated that avenanthramides biosynthesis and the hypersensitive response (HR) occurred in identical cells. Thus, the avenanthramides production may be one of sequential events programmed in HR leading to cell death. Furthermore, the phase of the defense response was different among mesophyll cells simultaneously treated with elicitor. These results suggest that individual cells may have different susceptibility to the elicitor.
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Affiliation(s)
- Yoshihiro Izumi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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77
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Stimpson AJ, Pereira RS, Kiss JZ, Correll MJ. Extraction and labeling methods for microarrays using small amounts of plant tissue. PHYSIOLOGIA PLANTARUM 2009; 135:229-236. [PMID: 19140889 DOI: 10.1111/j.1399-3054.2008.01191.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Procedures were developed to maximize the yield of high-quality RNA from small amounts of plant biomass for microarrays. Two disruption techniques (bead milling and pestle and mortar) were compared for the yield and the quality of RNA extracted from 1-week-old Arabidopsis thaliana seedlings (approximately 0.5-30 mg total biomass). The pestle and mortar method of extraction showed enhanced RNA quality at the smaller biomass samples compared with the bead milling technique, although the quality in the bead milling could be improved with additional cooling steps. The RNA extracted from the pestle and mortar technique was further tested to determine if the small quantity of RNA (500 ng-7 microg) was appropriate for microarray analyses. A new method of low-quantity RNA labeling for microarrays (NuGEN Technologies, Inc.) was used on five 7-day-old seedlings (approximately 2.5 mg fresh weight total) of Arabidopsis that were grown in the dark and exposed to 1 h of red light or continued dark. Microarray analyses were performed on a small plant sample (five seedlings; approximately 2.5 mg) using these methods and compared with extractions performed with larger biomass samples (approximately 500 roots). Many well-known light-regulated genes between the small plant samples and the larger biomass samples overlapped in expression changes, and the relative expression levels of selected genes were confirmed with quantitative real-time polymerase chain reaction, suggesting that these methods can be used for plant experiments where the biomass is extremely limited (i.e. spaceflight studies).
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Affiliation(s)
- Alexander J Stimpson
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, 32611, USA
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78
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Casson SA, Topping JF, Lindsey K. MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:857-869. [PMID: 19000164 DOI: 10.1111/j.1365-313x.2008.03738.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plant growth and development is dependent on the specification and maintenance of pools of stem cells found in the meristems. Mutations in the Arabidopsis MERISTEM-DEFECTIVE (MDF) gene lead to a loss of stem cell and meristematic activity in the root and vegetative shoot. MDF encodes a putative RS domain protein with a predicted role in transcription or RNA processing control. mdf mutants exhibit decreased levels of PINFORMED2 (PIN2) and PIN4 mRNAs, which is associated with a reduction in PIN:GFP levels, and with a defective auxin maximum in the basal region of the developing mdf embryo and seedling root meristem. Seedling roots also exhibit reduced PLETHORA (PLT), SCARECROW and SHORTROOT gene expression, a loss of stem cell activity, terminal differentiation of the root meristem and defective cell patterning. MDF expression is not defective in the bodenlos, pin1 or eir1/pin2 auxin mutants, and is not modulated by exogenous auxin. plt1 plt2 double mutants have unaffected levels of MDF RNA, indicating that MDF acts upstream of PIN and PLT gene expression. Differentiation of the shoot stem cell pool also occurs in mdf mutants, associated with a reduced WUSCHEL (WUS) expression domain and expanded CLAVATA3 (CLV3) domain. Overexpression of MDF leads to the activation of markers of embryonic identity and ectopic meristem activity in vegetative tissues. These results demonstrate a requirement for the MDF-dependent pathway in regulating PIN/PLT- and WUS/CLV-mediated meristem activity.
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Affiliation(s)
- Stuart A Casson
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham University, Durham, UK
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79
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Capron A, Chatfield S, Provart N, Berleth T. Embryogenesis: pattern formation from a single cell. THE ARABIDOPSIS BOOK 2009; 7:e0126. [PMID: 22303250 PMCID: PMC3243344 DOI: 10.1199/tab.0126] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
During embryogenesis a single cell gives rise to a functional multicellular organism. In higher plants, as in many other multicellular systems, essential architectural features, such as body axes and major tissue layers are established early in embryogenesis and serve as a positional framework for subsequent pattern elaboration. In Arabidopsis, the apicalbasal axis and the radial pattern of tissues wrapped around it are already recognizable in young embryos of only about a hundred cells in size. This early axial pattern seems to provide a coordinate system for the embryonic initiation of shoot and root. Findings from genetic studies in Arabidopsis are revealing molecular mechanisms underlying the initial establishment of the axial core pattern and its subsequent elaboration into functional shoots and roots. The genetic programs operating in the early embryo organize functional cell patterns rapidly and reproducibly from minimal cell numbers. Understanding their molecular details could therefore greatly expand our ability to generate plant body patterns de novo, with important implications for plant breeding and biotechnology.
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Affiliation(s)
- Arnaud Capron
- Dept. of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario, M5S 3G5 Canada
- Each of these authors contributed equally. Address correspondence to or
| | - Steven Chatfield
- Dept. of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario, M5S 3G5 Canada
- Each of these authors contributed equally. Address correspondence to or
| | - Nicholas Provart
- Dept. of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario, M5S 3G5 Canada
| | - Thomas Berleth
- Dept. of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario, M5S 3G5 Canada
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80
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Tauris B, Borg S, Gregersen PL, Holm PB. A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1333-47. [PMID: 19297552 PMCID: PMC2657541 DOI: 10.1093/jxb/erp023] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 01/07/2009] [Indexed: 05/19/2023]
Abstract
Nutrients destined for the developing cereal grain encounter several restricting barriers on their path towards their final storage sites in the grain. In order to identify transporters and chelating agents that may be involved in transport and deposition of zinc in the barley grain, expression profiles have been generated of four different tissue types: the transfer cells, the aleurone layer, the endosperm, and the embryo. Cells from these tissues were isolated with the 'laser capture microdissection' technology and the extracted RNA was subjected to three rounds of T7-based amplification. The amplified RNA was subsequently hybridized to Affymetrix 22K Barley GeneChips. Due to the short average length of the amplified transcripts and the positioning of numerous probe sets at locations more than 400 base pairs (bp) from the poly(A)-tail, a normalization approach was used where the probe positions were taken into account. On the basis of the expression levels of a number of metal homeostasis genes, a working model is proposed for the translocation of zinc from the phloem to the storage sites in the developing grain.
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Affiliation(s)
| | - Søren Borg
- To whom correspondence should be addressed:
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81
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Day RC, Herridge RP, Ambrose BA, Macknight RC. Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. PLANT PHYSIOLOGY 2008; 148:1964-84. [PMID: 18923020 PMCID: PMC2593665 DOI: 10.1104/pp.108.128108] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 10/06/2008] [Indexed: 05/18/2023]
Abstract
During the early stages of seed development, Arabidopsis (Arabidopsis thaliana) endosperm is syncytial and proliferates rapidly through repeated rounds of mitosis without cytokinesis. This stage of endosperm development is important in determining final seed size and is a model for studying aspects of cellular and molecular biology, such as the cell cycle and genomic imprinting. However, the small size of the Arabidopsis seed makes high-throughput molecular analysis of the early endosperm technically difficult. Laser capture microdissection enabled high-resolution transcript analysis of the syncytial stage of Arabidopsis endosperm development at 4 d after pollination. Analysis of Gene Ontology representation revealed a developmental program dominated by the expression of genes associated with cell cycle, DNA processing, chromatin assembly, protein synthesis, cytoskeleton- and microtubule-related processes, and cell/organelle biogenesis and organization. Analysis of core cell cycle genes implicates particular gene family members as playing important roles in controlling syncytial cell division. Hormone marker analysis indicates predominance for cytokinin signaling during early endosperm development. Comparisons with publicly available microarray data revealed that approximately 800 putative early seed-specific genes were preferentially expressed in the endosperm. Early seed expression was confirmed for 71 genes using quantitative reverse transcription-polymerase chain reaction, with 27 transcription factors being confirmed as early seed specific. Promoter-reporter lines confirmed endosperm-preferred expression at 4 d after pollination for five transcription factors, which validates the approach and suggests important roles for these genes during early endosperm development. In summary, the data generated provide a useful resource providing novel insight into early seed development and identify new target genes for further characterization.
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Affiliation(s)
- Robert C Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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82
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Gardner MJ, Baker AJ, Assie JM, Poethig RS, Haseloff JP, Webb AAR. GAL4 GFP enhancer trap lines for analysis of stomatal guard cell development and gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2008; 60:213-26. [PMID: 19033548 PMCID: PMC3071773 DOI: 10.1093/jxb/ern292] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 10/07/2008] [Accepted: 10/16/2008] [Indexed: 05/17/2023]
Abstract
To facilitate the monitoring of guard cells during development and isolation, a population of 704 GAL4 GFP enhancer trap lines was screened and four single insert lines with guard cell GFP expression and one with developmentally-regulated guard cell GFP expression were identified. The location of the T-DNA inserts, the expression of the flanking genes, and the promoter activity of the genomic DNA upstream of the T-DNA were characterized. The results indicated that the GFP expression pattern in at least one of the lines was due to elements in the intergenic DNA immediately upstream of the T-DNA, rather than due to the activity of the promoters of genes flanking the insert, and provide evidence for the involvement of Dof elements in regulating guard cell gene expression. It is shown further that the GAL4 GFP lines can be used to track the contribution of guard cell material in vitro, and this method was used to assess the purity of guard cell samples obtained using two methods of guard cell isolation.
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Affiliation(s)
- Michael J. Gardner
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andrew J. Baker
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Jean-Maurice Assie
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - R. Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jim P. Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alex A. R. Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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83
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Thiel J, Weier D, Sreenivasulu N, Strickert M, Weichert N, Melzer M, Czauderna T, Wobus U, Weber H, Weschke W. Different hormonal regulation of cellular differentiation and function in nucellar projection and endosperm transfer cells: a microdissection-based transcriptome study of young barley grains. PLANT PHYSIOLOGY 2008; 148:1436-52. [PMID: 18784282 PMCID: PMC2577268 DOI: 10.1104/pp.108.127001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 09/05/2008] [Indexed: 05/17/2023]
Abstract
Nucellar projection (NP) and endosperm transfer cells (ETC) are essential tissues in growing barley (Hordeum vulgare) grains, responsible for nutrient transfer from maternal to filial tissues, endosperm/embryo nutrition, and grain development. A laser microdissection pressure catapulting-based transcriptome analysis was established to study NP and ETC separately using a barley 12K macroarray. A major challenge was to isolate high-quality mRNA from preembedded, fixed tissue while maintaining tissue integrity. We show that probes generated from fixed and embedded tissue sections represent largely the transcriptome (>70%) of nonchemically treated and nonamplified references. In NP, the top-down gradient of cellular differentiation is reflected by the expression of C3HC4-type ubiquitin ligases and different histone genes, cell wall biosynthesis and expansin/extensin genes, as well as genes involved in programmed cell death-related proteolysis coupled to nitrogen remobilization, indicating distinct areas simultaneously undergoing mitosis, cell elongation, and disintegration. Activated gene expression related to gibberellin synthesis and function suggests a regulatory role for gibberellins in establishment of the differentiation gradient. Up-regulation of plasmalemma-intrinsic protein and tonoplast-intrinsic protein genes indicates involvement in nutrient transfer and/or unloading. In ETC, AP2/EREBP-like transcription factors and ethylene functions are transcriptionally activated, a response possibly coupled to activated defense mechanisms. Transcriptional activation of nucleotide sugar metabolism may be attributed to ascorbate synthesis and/or cell wall biosynthesis. These processes are potentially controlled by trehalose-6-P synthase/phosphatase, as suggested by expression of their respective genes. Up-regulation of amino acid permeases in ETC indicates important roles in active nutrient uptake from the apoplastic space into the endosperm.
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Affiliation(s)
- Johannes Thiel
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, D-06466 Gatersleben, Germany.
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84
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Suwabe K, Suzuki G, Takahashi H, Shiono K, Endo M, Yano K, Fujita M, Masuko H, Saito H, Fujioka T, Kaneko F, Kazama T, Mizuta Y, Kawagishi-Kobayashi M, Tsutsumi N, Kurata N, Nakazono M, Watanabe M. Separated transcriptomes of male gametophyte and tapetum in rice: validity of a laser microdissection (LM) microarray. PLANT & CELL PHYSIOLOGY 2008; 49:1407-16. [PMID: 18755754 PMCID: PMC2566930 DOI: 10.1093/pcp/pcn124] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Accepted: 08/15/2008] [Indexed: 05/19/2023]
Abstract
In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. Expression profiles of 11 known tapetum specific-genes were consistent with previous reports. Based on their spatial and temporal expression patterns, 140 genes which had been previously defined as anther specific were further classified as male gametophyte specific (71 genes, 51%), tapetum-specific (seven genes, 5%) or expressed in both male gametophyte and tapetum (62 genes, 44%). These results indicate that the 44K LM-microarray is a reliable tool to analyze the gene expression profiles of two important cell types in the anther, the microspore/pollen and tapetum.
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Affiliation(s)
- Keita Suwabe
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582 Japan
| | - Hirokazu Takahashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Katsuhiro Shiono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Makoto Endo
- Laboratory of Biotechnology, National Institute of Crop Science, Tsukuba, 305-8518 Japan
| | - Kentaro Yano
- Faculty of Agriculture, Meiji University, Kawasaki, 214-8571 Japan
| | - Masahiro Fujita
- Plant Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Hiromi Masuko
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Hiroshi Saito
- The 21st Century Center of Excellence Program, Iwate University, Morioka, 020-8550 Japan
| | - Tomoaki Fujioka
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Fumi Kaneko
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Tomohiko Kazama
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
- The 21st Century Center of Excellence Program, Iwate University, Morioka, 020-8550 Japan
| | - Yoko Mizuta
- Plant Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | | | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Mikio Nakazono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Masao Watanabe
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
- The 21st Century Center of Excellence Program, Iwate University, Morioka, 020-8550 Japan
- Faculty of Science, Tohoku University, Sendai, 980-8578 Japan
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85
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McGarry RC, Ayre BG. A DNA element between At4g28630 and At4g28640 confers companion-cell specific expression following the sink-to-source transition in mature minor vein phloem. PLANTA 2008; 228:839-49. [PMID: 18682980 DOI: 10.1007/s00425-008-0786-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Accepted: 07/04/2008] [Indexed: 05/05/2023]
Abstract
The collection phloem in minor veins is distinct from other vein classes in that the minor veins mature during the sink to source transition and are the primary sites of phloem loading. After maturation, minor vein phloem maintains its character in part through minor-vein specific regulatory cascades; however despite its physiological significance, little of these developmental programs is understood. From an Arabidopsis enhancer trap screen, we identified MATURE MINOR VEIN ELEMENT1 (MMVE1) in the intergenic region between two oppositely oriented genes, the ABC transporter ATM1 (At4g28630) and IAA11 (At4g28640). MMVE1 promotes reporter gene activity in minor vein phloem in a pattern resembling the sink to source transition. Promoter truncation experiments and phylogenetic footprinting demonstrate sequences proximal to ATM1 promote minor vein expression whereas sequences closer to IAA11 repress it. Both orientations of the promoter were used to drive expression of CONSTANS to generate a phloem mobile signal conferring early flowering under non-inductive conditions. Tandem copies of MMVE1 increase minor vein expression strength and specificity. MMVE1 is the first minor vein enhancer characterized from a species that loads from the apoplast, and supports the presence of unique regulatory cascades operating in minor vein phloem.
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Affiliation(s)
- Roisin C McGarry
- Department of Biological Sciences, University of North Texas, 1504 W. Mulberry, SRB Rm 120, P.O. Box 305220, Denton, TX 76203 5220, USA.
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86
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Passarinho P, Ketelaar T, Xing M, van Arkel J, Maliepaard C, Hendriks MW, Joosen R, Lammers M, Herdies L, den Boer B, van der Geest L, Boutilier K. BABY BOOM target genes provide diverse entry points into cell proliferation and cell growth pathways. PLANT MOLECULAR BIOLOGY 2008; 68:225-37. [PMID: 18663586 DOI: 10.1007/s11103-008-9364-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 06/05/2008] [Indexed: 05/22/2023]
Abstract
Ectopic expression of the Brassica napus BABY BOOM (BBM) AP2/ERF transcription factor is sufficient to induce spontaneous cell proliferation leading primarily to somatic embryogenesis, but also to organogenesis and callus formation. We used DNA microarray analysis in combination with a post-translationally regulated BBM:GR protein and cycloheximide to identify target genes that are directly activated by BBM expression in Arabidopsis seedlings. We show that BBM activated the expression of a largely uncharacterized set of genes encoding proteins with potential roles in transcription, cellular signaling, cell wall biosynthesis and targeted protein turnover. A number of the target genes have been shown to be expressed in meristems or to be involved in cell wall modifications associated with dividing/growing cells. One of the BBM target genes encodes an ADF/cofilin protein, ACTIN DEPOLYMERIZING FACTOR9 (ADF9). The consequences of BBM:GR activation on the actin cytoskeleton were followed using the GFP:FIMBRIN ACTIN BINDING DOMAIN2 (GFP:FABD) actin marker. Dexamethasone-mediated BBM:GR activation induced dramatic changes in actin organization resulting in the formation of dense actin networks with high turnover rates, a phenotype that is consistent with cells that are rapidly undergoing cytoplasmic reorganization. Together the data suggest that the BBM transcription factor activates a complex network of developmental pathways associated with cell proliferation and growth.
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Affiliation(s)
- Paul Passarinho
- Plant Research International, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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87
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Deeken R, Ache P, Kajahn I, Klinkenberg J, Bringmann G, Hedrich R. Identification of Arabidopsis thaliana phloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:746-59. [PMID: 18485061 DOI: 10.1111/j.1365-313x.2008.03555.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Phloem-mobile signals play a major role in plant nutrition, development and communication. In the latter context, phloem-mobile RNAs have been associated with signalling between plant tissues. In this study, we focused on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. To isolate transcripts expressed in phloem parenchyma cells and in companion cell-sieve element complexes, we used laser microdissection coupled to laser pressure catapulting (LMPC). Mobile transcripts in sieve elements were isolated from leaf phloem exudates. After optimization of sampling and fixation, RNA of high quality was isolated from both sources. The modifications to the RNA amplification procedure described here were well suited to production of RNA of sufficient yield and quality for microarray experiments. Microarrays hybridized with LMPC-derived phloem tissue or phloem sap RNA allowed differentiation between phloem-expressed and mobile transcript species. Using this set of phloem transcripts and comparing them with microarrays derived from databases of light, hormone and nutrient treatment experiments, we identified phloem-derived RNAs as mobile, potential long-distance signals. Our dataset thus provides a search criterion for phloem-based signals hidden in the complex datasets of microarray experiments. The availability of these comprehensive phloem transcript profiles will facilitate reverse-genetic studies and forward-genetic screens for phloem and long-distance RNA signalling mutants.
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Affiliation(s)
- Rosalia Deeken
- Julius-von-Sachs-Institute for Biosciences, University of Würzburg, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
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88
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Cai S, Lashbrook CC. Stamen abscission zone transcriptome profiling reveals new candidates for abscission control: enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2. PLANT PHYSIOLOGY 2008; 146:1305-21. [PMID: 18192438 PMCID: PMC2259061 DOI: 10.1104/pp.107.110908] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 01/08/2008] [Indexed: 05/18/2023]
Abstract
Organ detachment requires cell separation within abscission zones (AZs). Physiological studies have established that ethylene and auxin contribute to cell separation control. Genetic analyses of abscission mutants have defined ethylene-independent detachment regulators. Functional genomic strategies leading to global understandings of abscission have awaited methods for isolating AZ cells of low abundance and very small size. Here, we couple laser capture microdissection of Arabidopsis thaliana stamen AZs and GeneChip profiling to reveal the AZ transcriptome responding to a developmental shedding cue. Analyses focus on 551 AZ genes (AZ(551)) regulated at the highest statistical significance (P < or = 0.0001) over five floral stages linking prepollination to stamen shed. AZ(551) includes mediators of ethylene and auxin signaling as well as receptor-like kinases and extracellular ligands thought to act independent of ethylene. We hypothesized that novel abscission regulators might reside in disproportionately represented Gene Ontology Consortium functional categories for cell wall modifying proteins, extracellular regulators, and nuclear-residing transcription factors. Promoter-beta-glucuronidase expression of one transcription factor candidate, ZINC FINGER PROTEIN2 (AtZFP2), was elevated in stamen, petal, and sepal AZs. Flower parts of transgenic lines overexpressing AtZFP2 exhibited asynchronous and delayed abscission. Abscission defects were accompanied by altered floral morphology limiting pollination and fertility. Hand-pollination restored transgenic fruit development but not the rapid abscission seen in wild-type plants, demonstrating that pollination does not assure normal rates of detachment. In wild-type stamen AZs, AtZFP2 is significantly up-regulated postanthesis. Phenotype data from transgene overexpression studies suggest that AtZFP2 participates in processes that directly or indirectly influence organ shed.
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Affiliation(s)
- Suqin Cai
- Department of Horticulture, Iowa State University, Ames, IA 50011-1100, USA
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89
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Chandler J, Nardmann J, Werr W. Plant development revolves around axes. TRENDS IN PLANT SCIENCE 2008; 13:78-84. [PMID: 18262821 DOI: 10.1016/j.tplants.2007.11.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 11/19/2007] [Accepted: 11/19/2007] [Indexed: 05/06/2023]
Abstract
Arabidopsis thaliana has become a paradigm for dicot embryo development, despite its embryology being non-representative of dicots in general. The recent cloning of heterologous genes involved in embryonic development from maize and construction of robust phylogenies has shed light on the conservation of transcription factor function and now facilitates a comparison of maize and Arabidopsis embryogenesis orthology. In this review, we focus on a comparison of expression domains of WUSCHEL HOMEOBOX LIKE (WOX), SHOOTMERISTEMLESS (STM), DORNROESCHEN (DRN) and CUP-SHAPED COTYLEDON (CUC) genes and their role in axialization in both species, showing that despite significantly divergent modes of embryogenesis, most notably in terms of axes and planes of symmetry, there is considerable conservation of function as well as notable differences between maize and Arabidopsis.
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Affiliation(s)
- John Chandler
- Institute of Developmental Biology, University of Cologne, Cologne, Germany
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90
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Casson SA, Spencer MWB, Lindsey K. Laser-capture microdissection to study global transcriptional changes during plant embryogenesis. Methods Mol Biol 2008; 427:111-20. [PMID: 18370001 DOI: 10.1007/978-1-59745-273-1_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
A key objective in the study of plant embryogenesis is to identify genes expressed in temporal and spatial patterns during development, in order to understand transcriptional control mechanisms regulating pattern formation, differentiation and morphogenesis. Mutagenic approaches have proved powerful to identify essential genes, but global, transcriptome-wide analysis of mRNA profiles in cells at different stages of differentiation would allow the identification of changes in the abundance of major classes of transcripts expressed from genes that are known to respond to regulatory signals, such as hormones. Particular classes of transcription factors or other genes might also be discovered to be associated with particular aspects of cell differentiation. This information would allow the construction of models to describe how signalling pathways might modulate transcriptional changes associated with cell differentiation. Previous limitations in tissue accessibility for RNA isolation have been overcome through the use of laser-capture microdissection, which allows cells from different embryonic tissues to be isolated, for RNA isolation, amplification and analysis by either polymerase chain reaction or DNA microarray techniques.
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Affiliation(s)
- Stuart A Casson
- The Integrative Cell Biology Laboratory, Durham University, UK
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91
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Hölscher D, Schneider B. Application of Laser-Assisted Microdissection for Tissue and Cell-Specific Analysis of RNA, Proteins, and Metabolites. PROGRESS IN BOTANY 2008. [DOI: 10.1007/978-3-540-72954-9_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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92
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Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF. A majority of cotton genes are expressed in single-celled fiber. PLANTA 2008; 227:319-29. [PMID: 17849148 DOI: 10.1007/s00425-007-0619-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 08/24/2007] [Indexed: 05/11/2023]
Abstract
Multicellular eukaryotes contain a diversity of cell types, presumably differing from one another in the suite of genes expressed during development. At present, little is known about the proportion of the genome transcribed in most cell types, nor the degree to which global patterns of expression change during cellular differentiation. To address these questions in a model plant system, we studied the unique and highly exaggerated single-celled, epidermal seed trichomes ("cotton") of cultivated cotton (Gossypium hirsutum). By taking advantage of advances in expression profiling and microarray technology, we evaluated the transcriptome of cotton fibers across a developmental time-course, from a few days post-anthesis through primary and secondary wall synthesis stages. Comparisons of gene expression in populations of developing cotton fiber cells to genetically complex reference samples derived from 6 different cotton organs demonstrated that a remarkably high proportion of the cotton genome is transcribed, with 75-94% of the total genome transcribed at each stage. Compared to the reference samples, more than half of all genes were up-regulated during at least one stage of fiber development. These genes were clustered into seven groups of expression profiles that provided new insight into biological processes governing fiber development. Genes implicated in vesicle coating and trafficking were found to be overexpressed throughout all stages of fiber development studied, indicating their important role in maintaining rapid growth of this unique plant cell.
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Affiliation(s)
- Ran Hovav
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
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93
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Curtis MD, Grossniklaus U. Molecular control of autonomous embryo and endosperm development. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s00497-007-0061-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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94
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Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MCP, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:391-404. [PMID: 17764504 PMCID: PMC2156186 DOI: 10.1111/j.1365-313x.2007.03244.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.
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Affiliation(s)
- Kazuhiro Ohtsu
- Department of Agronomy, Iowa State UniversityAmes, IA 50011, USA
| | - Marianne B Smith
- Department of Agronomy, Iowa State UniversityAmes, IA 50011, USA
| | - Scott J Emrich
- Bioinformatics and Computational Biology Graduate Program, Iowa State UniversityAmes, IA 50011, USA
| | - Lisa A Borsuk
- Bioinformatics and Computational Biology Graduate Program, Iowa State UniversityAmes, IA 50011, USA
| | - Ruilian Zhou
- Department of Agronomy, Iowa State UniversityAmes, IA 50011, USA
| | - Tianle Chen
- Plant Biology Department, University of GeorgiaAthens, GA 30602, USA
| | - Xiaolan Zhang
- Plant Biology Department, University of GeorgiaAthens, GA 30602, USA
| | | | - Jon Beck
- Division of Mathematics and Computer Science, Truman State UniversityKirksville, MO 63501, USA
| | - Brent Buckner
- Division of Science, Truman State UniversityKirksville, MO 63501, USA
| | | | - Dan Nettleton
- Bioinformatics and Computational Biology Graduate Program, Iowa State UniversityAmes, IA 50011, USA
- Department of Statistics, Iowa State UniversityAmes, IA 50011, USA
- Center for Plant Genomics, Iowa State UniversityAmes, IA 50011, USA
| | - Michael J Scanlon
- Plant Biology Department, University of GeorgiaAthens, GA 30602, USA
- Department of Plant Biology, Cornell UniversityIthaca, NY 14853, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State UniversityAmes, IA 50011, USA
- Bioinformatics and Computational Biology Graduate Program, Iowa State UniversityAmes, IA 50011, USA
- Center for Plant Genomics, Iowa State UniversityAmes, IA 50011, USA
- (fax +1 515 294 5256; e-mail )
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95
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Wu Y, Llewellyn DJ, White R, Ruggiero K, Al-Ghazi Y, Dennis ES. Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules. PLANTA 2007; 226:1475-90. [PMID: 17636323 DOI: 10.1007/s00425-007-0580-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 06/25/2007] [Indexed: 05/12/2023]
Abstract
Cotton (Gossypium hirsutum L.) fibre initial cells undergo a rapid cellular re-programming around anthesis to form the long cellulose fibres prized for textile manufacture. On the day of anthesis the cotton fibre initial cells balloon out from the ovule surface and so are clearly distinguished from adjacent epidermal pavement cells. To enhance our understanding of the molecular processes that determine which cells become fibres and why adjacent epidermal cells remain in a different developmental state we studied the expression profiles of the two respective cell types. Using laser-capture microdissection, coupled with an in vitro RNA amplification system, we used cDNA microarray slides to profile the gene expression in expanding fibre initials compared to the non-expanding epidermal cells at an early stage just after the fibre initials are discernable. Except for a few regulatory genes, the genes that are up-regulated in the cotton fibre initials relative to epidermal cells predominantly encode proteins involved in generating the components for the extra cell membrane and primary cell wall needed for the rapid cell expansion of the initials. This includes synthesis of enzymes and cell wall proteins, carbohydrates, and lipids. An analysis of single channel fluorescence levels confirmed that these classes of genes were also the most highly expressed genes in fibre initials. Genes involved in DNA metabolism were also well represented in the expanding fibre cell, consistent with the limited endoreduplication we previously reported to occur in fibre initial cells.
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Affiliation(s)
- Yingru Wu
- CSIRO Plant Industry, P.O. Box 1600, Canberra, ACT 2601, Australia
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96
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Alves-Ferreira M, Wellmer F, Banhara A, Kumar V, Riechmann JL, Meyerowitz EM. Global expression profiling applied to the analysis of Arabidopsis stamen development. PLANT PHYSIOLOGY 2007; 145:747-62. [PMID: 17905860 PMCID: PMC2048804 DOI: 10.1104/pp.107.104422] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 09/14/2007] [Indexed: 05/17/2023]
Abstract
To obtain detailed information about gene expression during stamen development in Arabidopsis (Arabidopsis thaliana), we compared, by microarray analysis, the gene expression profile of wild-type inflorescences to those of the floral mutants apetala3, sporocyteless/nozzle, and male sterile1 (ms1), in which different aspects of stamen formation are disrupted. These experiments led to the identification of groups of genes with predicted expression at early, intermediate, and late stages of stamen development. Validation experiments using in situ hybridization confirmed the predicted expression patterns. Additional experiments aimed at characterizing gene expression specifically during microspore formation. To this end, we compared the gene expression profiles of wild-type flowers of distinct developmental stages to those of the ms1 mutant. Computational analysis of the datasets derived from this experiment led to the identification of genes that are likely involved in the control of key developmental processes during microsporogenesis. We also identified a large number of genes whose expression is prolonged in ms1 mutant flowers compared to the wild type. This result suggests that MS1, which encodes a putative transcriptional regulator, is involved in the stage-specific repression of these genes. Lastly, we applied reverse genetics to characterize several of the genes identified in the microarray experiments and uncovered novel regulators of microsporogenesis, including the transcription factor MYB99 and a putative phosphatidylinositol 4-kinase.
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Affiliation(s)
- Márcio Alves-Ferreira
- California Institute of Technology, Division of Biology, Pasadena, California 91125, USA
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97
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Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ. An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS One 2007; 2:e718. [PMID: 17684564 PMCID: PMC1934936 DOI: 10.1371/journal.pone.0000718] [Citation(s) in RCA: 1845] [Impact Index Per Article: 108.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 06/28/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way. METHODOLOGY/PRINCIPAL FINDINGS In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph - or eFP - Browser, available at http://www.bar.utoronto.ca/, for exploring microarray and other data for hypothesis generation. This eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. We give examples of using the tool to present Arabidopsis gene expression data from the AtGenExpress Consortium (Arabidopsis eFP Browser), data for subcellular localization of Arabidopsis proteins (Cell eFP Browser), and mouse tissue atlas microarray data (Mouse eFP Browser). CONCLUSIONS/SIGNIFICANCE The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.
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Affiliation(s)
- Debbie Winter
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ben Vinegar
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Hardeep Nahal
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ron Ammar
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Greg V. Wilson
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas J. Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- * To whom correspondence should be addressed. E-mail:
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98
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De Smet I, Jürgens G. Patterning the axis in plants – auxin in control. Curr Opin Genet Dev 2007; 17:337-43. [PMID: 17627808 DOI: 10.1016/j.gde.2007.04.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 04/26/2007] [Accepted: 04/29/2007] [Indexed: 01/23/2023]
Abstract
Axis formation and patterning are fundamental processes establishing the body organization of multicellular organisms. In plants, patterning is not confined to embryogenesis but continues to produce new structures--lateral organs--along the growing primary body axis and also initiates secondary body axes. The signalling molecule auxin has been identified as a key player in plant axial patterning. The shoot and root sections of the axis seem to produce lateral organs in different ways. However, very recent findings suggest a general mechanism of branching triggered by local accumulation of auxin in a 'zone of competence' at the margin of stem-cell systems. How the general auxin signal is converted into organ-specific developmental programs remains a major challenge for the future.
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Affiliation(s)
- Ive De Smet
- Centre for Plant Molecular Biology (ZMBP), Developmental Genetics, Tübingen University, Auf der Morgenstelle 3, D-72076 Tübingen, Germany.
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99
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Le BH, Wagmaister JA, Kawashima T, Bui AQ, Harada JJ, Goldberg RB. Using genomics to study legume seed development. PLANT PHYSIOLOGY 2007; 144:562-74. [PMID: 17556519 PMCID: PMC1914191 DOI: 10.1104/pp.107.100362] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 04/18/2007] [Indexed: 05/15/2023]
Affiliation(s)
- Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095, USA
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100
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Zhang X, Madi S, Borsuk L, Nettleton D, Elshire RJ, Buckner B, Janick-Buckner D, Beck J, Timmermans M, Schnable PS, Scanlon MJ. Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. PLoS Genet 2007; 3:e101. [PMID: 17571927 PMCID: PMC1904365 DOI: 10.1371/journal.pgen.0030101] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Accepted: 05/07/2007] [Indexed: 12/28/2022] Open
Abstract
Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional networks that are hidden within large microarray datasets. Microarray analyses in which mutant organisms are compared to nonmutant siblings can be especially problematic when the gene of interest is expressed in relatively few cells. Here, we describe the use of laser microdissection microarray to perform transcriptional profiling of the maize shoot apical meristem (SAM), a ~100-μm pillar of organogenic cells that is required for leaf initiation. Microarray analyses compared differential gene expression within the SAM and incipient leaf primordium of nonmutant and narrow sheath mutant plants, which harbored mutations in the duplicate genes narrow sheath1 (ns1) and narrow sheath2 (ns2). Expressed in eight to ten cells within the SAM, ns1 and ns2 encode paralogous WUSCHEL1-like homeobox (WOX) transcription factors required for recruitment of leaf initials that give rise to a large lateral domain within maize leaves. The data illustrate the utility of laser microdissection-microarray analyses to identify a relatively small number of genes that are differentially expressed within the SAM. Moreover, these analyses reveal potentially conserved WOX gene functions and implicate specific hormonal and signaling pathways during early events in maize leaf development. Unlike animals, plants exhibit a prolonged period of organogenesis, generating new leaves throughout their life cycle. This ability to maintain an embryo-like state is dependent upon the activity of shoot meristems, whose dual functions are to supply an inner core of pluripotent cells that sustain the shoot meristem while simultaneously generating new leaves derived from cells at the meristem periphery. Deciphering the complex combinations of molecular signals that transform meristematic cells into leaf primordia is a central question in plant developmental biology. In this study, we used the power of focused laser light to microdissect shoot meristems from neighboring leaf and stem tissue in the maize plant. Once isolated, we compared patterns of gene expression in normal shoot meristems to those of genetically mutant shoot meristems that form abnormal, narrow leaves. Out of more than 21,000 maize genes analyzed, 66 genes were identified as misexpressed in the mutant shoot meristems. All but one of the differentially expressed genes are previously unstudied in maize, and the majority are predicted to function during cell division, growth, or developmental signaling. Many of these novel genes are expressed in specific domains of the shoot meristem, consistent with their predicted function during maize leaf initiation.
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Affiliation(s)
- Xiaolan Zhang
- Plant Biology Department, University of Georgia, Athens, Georgia, United States of America
| | - Shahinez Madi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lisa Borsuk
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Robert J Elshire
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Brent Buckner
- Division of Science, Truman State University, Kirksville, Missouri, United States of America
| | - Diane Janick-Buckner
- Division of Science, Truman State University, Kirksville, Missouri, United States of America
| | - Jon Beck
- Division of Mathematics and Computer Science, Truman State University, Kirksville, Missouri, United States of America
| | - Marja Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Patrick S Schnable
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Michael J Scanlon
- Plant Biology Department, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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