51
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Cnudde F, Hedatale V, de Jong H, Pierson ES, Rainey DY, Zabeau M, Weterings K, Gerats T, Peters JL. Changes in gene expression during male meiosis in Petunia hybrida. Chromosome Res 2007; 14:919-32. [PMID: 17203374 DOI: 10.1007/s10577-006-1099-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/06/2006] [Accepted: 11/06/2006] [Indexed: 12/17/2022]
Abstract
We analyzed changes in gene expression during male meiosis in Petunia by combining the meiotic staging of pollen mother cells from a single anther with cDNA-AFLP transcript profiling of mRNA from the synchronously developing sister anthers. The transcript profiling experiments focused on the identification of genes with a modulated expression profile during meiosis, while premeiotic archesporial cells and postmeiotic microspores served as a reference. About 8000 transcript tags, estimated at 30% of the total transcriptome, were generated, of which around 6% exhibited a modulated gene expression pattern at meiosis. Cluster analysis revealed a transcriptional cascade that coincides with the initiation and progression through all stages of the two meiotic divisions. Fragments that exhibited high expression specifically during meiosis I were characterized further by sequencing; 90 out of the 293 sequenced fragments showed homology with known genes, belonging to a wide range of gene classes, including previously characterized meiotic genes. In-situ hybridization experiments were performed to determine the spatial expression pattern for five selected transcript tags. Its concurrence with cDNA-AFLP transcript profiles indicates that this is an excellent approach to study genes involved in specialized processes such as meiosis. Our data set provides the potential to unravel unique meiotic genes that are as yet elusive to reverse genetics approaches.
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Affiliation(s)
- Filip Cnudde
- Institute for Wetland and Water Research, Department of Experimental Botany, Section Plant Genetics, Radboud University, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
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52
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Vandeputte O, Vereecke D, Mol A, Lenjou M, Van Bockstaele D, El Jaziri M, Baucher M. Rhodococcus fascians infection accelerates progression of tobacco BY-2 cells into mitosis through rapid changes in plant gene expression. THE NEW PHYTOLOGIST 2007; 175:140-154. [PMID: 17547674 DOI: 10.1111/j.1469-8137.2007.02062.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
* To characterize plant cell cycle activation following Rhodococcus fascians infection, bacterial impact on cell cycle progression of tobacco BY-2 cells was investigated. * S-phase-synchronized BY-2 cells were cocultivated with R. fascians and cell cycle progression was monitored by measuring mitotic index, cell cycle gene expression and flow cytometry parameters. Cell cycle alteration was further investigated by cDNA-AFLP (amplified fragment length polymorphism). * It was shown that cell cycle progression of BY-2 cells was accelerated only upon infection with bacteria whose virulence gene expression was induced by a leafy gall extract. Thirty-eight BY-2 genes showed a differential expression within 6 h post-infection. Among these, seven were previously associated with specific plant cell cycle phases (in particular S and G2/M phases). Several genes also showed a differential expression during leafy gall formation. * R. fascians-infected BY-2 cells provide a simple model to identify plant genes related to leafy gall development. R. fascians can also be regarded as a useful biotic agent to alter cell cycle progression and, thereby, gain a better understanding of cell cycle regulation in plants.
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Affiliation(s)
- Olivier Vandeputte
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, B-6041 Gosselies, Belgium
| | - Danny Vereecke
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB)
| | - Adeline Mol
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, B-6041 Gosselies, Belgium
| | - Marc Lenjou
- Laboratory of Experimental Haematology, University of Antwerp, Antwerp University Hospital, Wilrijkstraat 10, B-2650 Edegem, Belgium
| | - Dirk Van Bockstaele
- Laboratory of Experimental Haematology, University of Antwerp, Antwerp University Hospital, Wilrijkstraat 10, B-2650 Edegem, Belgium
| | - Mondher El Jaziri
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, B-6041 Gosselies, Belgium
| | - Marie Baucher
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, B-6041 Gosselies, Belgium
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53
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Van Damme D, Coutuer S, De Rycke R, Bouget FY, Inzé D, Geelen D. Somatic cytokinesis and pollen maturation in Arabidopsis depend on TPLATE, which has domains similar to coat proteins. THE PLANT CELL 2006; 18:3502-18. [PMID: 17189342 PMCID: PMC1785392 DOI: 10.1105/tpc.106.040923] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
TPLATE was previously identified as a potential cytokinesis protein targeted to the cell plate. Disruption of TPLATE in Arabidopsis thaliana leads to the production of shriveled pollen unable to germinate. Vesicular compartmentalization of the mature pollen is dramatically altered, and large callose deposits accumulate near the intine cell wall layer. Green fluorescent protein (GFP)-tagged TPLATE expression under the control of the pollen promoter Lat52 complements the phenotype. Downregulation of TPLATE in Arabidopsis seedlings and tobacco (Nicotiana tabacum) BY-2 suspension cells results in crooked cell walls and cell plates that fail to insert into the mother wall. Besides accumulating at the cell plate, GFP-fused TPLATE is temporally targeted to a narrow zone at the cell cortex where the cell plate connects to the mother wall. TPLATE-GFP also localizes to subcellular structures that accumulate at the pollen tube exit site in germinating pollen. Ectopic callose depositions observed in mutant pollen also occur in RNA interference plants, suggesting that TPLATE is implicated in cell wall modification. TPLATE contains domains similar to adaptin and beta-COP coat proteins. These data suggest that TPLATE functions in vesicle-trafficking events required for site-specific cell wall modifications during pollen germination and for anchoring of the cell plate to the mother wall at the correct cortical position.
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Affiliation(s)
- Daniël Van Damme
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnologie, Ghent University, B-9052 Gent, Belgium
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54
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Abstract
Cell cycle regulation is of pivotal importance for plant growth and development. Although plant cell division shares basic mechanisms with all eukaryotes, plants have evolved novel molecules orchestrating the cell cycle. Some regulatory proteins, such as cyclins and inhibitors of cyclin-dependent kinases, are particularly numerous in plants, possibly reflecting the remarkable ability of plants to modulate their postembryonic development. Many plant cells also can continue DNA replication in the absence of mitosis, a process known as endoreduplication, causing polyploidy. Here, we review the molecular mechanisms that regulate cell division and endoreduplication and we discuss our understanding, albeit very limited, on how the cell cycle is integrated with plant development.
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Affiliation(s)
- Dirk Inzé
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
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55
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Matsubara S, Hurry V, Druart N, Benedict C, Janzik I, Chavarría-Krauser A, Walter A, Schurr U. Nocturnal changes in leaf growth of Populus deltoides are controlled by cytoplasmic growth. PLANTA 2006; 223:1315-28. [PMID: 16333638 DOI: 10.1007/s00425-005-0181-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 10/18/2005] [Indexed: 05/05/2023]
Abstract
Growing leaves do not expand at a constant rate but exhibit pronounced diel growth rhythms. However, the mechanisms giving rise to distinct diel growth dynamics in different species are still largely unknown. As a first step towards identifying genes controlling rate and timing of leaf growth, we analysed the transcriptomes of rapidly expanding and fully expanded leaves of Populus deltoides Bartr. ex. Marsh at points of high and low expansion at night. Tissues with well defined temporal growth rates were harvested using an online growth-monitoring system based on a digital image sequence processing method developed for quantitative mapping of dicot leaf growth. Unlike plants studied previously, leaf growth in P. deltoides was characterised by lack of a base-tip gradient across the lamina, and by maximal and minimal growth at dusk and dawn, respectively. Microarray analysis revealed that the nocturnal decline in growth coincided with a concerted down-regulation of ribosomal protein genes, indicating deceleration of cytoplasmic growth. In a subsequent time-course experiment, Northern blotting and real-time RT-PCR confirmed that the ribosomal protein gene RPL12 and a cell-cycle gene H2B were down-regulated after midnight following a decrease in cellular carbohydrate concentrations. Thus, we propose that the spatio-temporal growth pattern in leaves of P. deltoides primarily arises from cytoplasmic growth whose activity increases from afternoon to midnight and thereafter decreases in this species.
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Affiliation(s)
- Shizue Matsubara
- Institut for Chemistry and Dynamics of the Geosphere: Phytosphere (ICG-III), Research Centre Jülich, 52425 Jülich, Germany.
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56
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Jen CH, Manfield IW, Michalopoulos I, Pinney JW, Willats WGT, Gilmartin PM, Westhead DR. The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:336-48. [PMID: 16623895 DOI: 10.1111/j.1365-313x.2006.02681.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (ACT), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Results are accompanied by estimates of the statistical significance of the correlation relationships, expressed as probability (P) and expectation (E) values. Additionally, highly ranked genes on a correlation list can be examined using the novel clique finder tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots, and dissection into cliques of co-regulated genes. We illustrate the applications of the software by analysing genes encoding functionally related proteins, as well as pathways involved in plant responses to environmental stimuli. These analyses demonstrate novel biological relationships underlying the observed gene co-expression patterns. To demonstrate the ability of the software to develop testable hypotheses on gene function within a defined biological process we have used the example of cell wall biosynthesis genes. The resource is freely available at http://www.arabidopsis.leeds.ac.uk/ACT/
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Affiliation(s)
- Chih-Hung Jen
- School of Biochemistry and Microbiology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
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57
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Fiorani F, Beemster GTS. Quantitative analyses of cell division in plants. PLANT MOLECULAR BIOLOGY 2006; 60:963-79. [PMID: 16724264 DOI: 10.1007/s11103-005-4065-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 10/13/2005] [Indexed: 05/08/2023]
Abstract
At the molecular level regulatory interactions between cell cycle genes are being uncovered rapidly, but less progress is made in unravelling how these molecular events regulate growth processes at the level of cells and of the whole organism. The main obstacle is the absence of a set of analytical tools that are powerful enough to determine pertinent parameters and, at the same time, relatively easy to use by non-specialized laboratories. Appropriate methodology to obtain this type of data has been pioneered in the first half of the last century and is now commonly defined as 'kinematic analysis'. Unfortunately, the laborious nature of these analyses and the relatively complex numerical methods used, have limited their use to only a handful of specialized research groups. In this article we attempt to present an accessible entry to this methodology, particularly in terms of the mathematical framework. We start describing the simplest possible system, i.e., a virtually homogenous cell suspension culture. Then, we outline the analysis of dicotyledonous leaves, root tips, monocotyledonous leaves, and finally shoot apical meristems. For each of these systems we discuss the details of the calculation of cell division parameters such as cell cycle duration, size of the meristem and number of cells contained in it, which enables answering fundamental questions about the relative contribution of differences in cell production and cell size to variation in growth. In addition, we discuss the assumptions and limitations of these and alternative methodologies with the aim to facilitate the choice of appropriate analyses depending on the specific research question.
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Affiliation(s)
- Fabio Fiorani
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB)/University of Ghent, Technologiepark 927, Ghent, Belgium
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58
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Vuylsteke M, Daele H, Vercauteren A, Zabeau M, Kuiper M. Genetic dissection of transcriptional regulation by cDNA-AFLP. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 45:439-46. [PMID: 16412088 DOI: 10.1111/j.1365-313x.2005.02630.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This study demonstrates that cDNA-AFLP is a powerful gel-based genome-scale transcript profiling technique to generate quantitative gene expression profiles for eQTL mapping. We used cDNA-AFLP to monitor the relative abundance of 912 transcripts across 50 Arabidopsis thaliana recombinant inbred lines. Estimates for heritability of cDNA-AFLP intensity polymorphisms were high, with a median of 0.30 and an interquartile range of 0.21-0.44. A total of 198 expression polymorphisms were significantly linked to specific chromosomal regions (P < 0.05). Both cis- and trans-acting loci correlated with the variation in gene expression levels were found. Some of the trans-acting loci correlated to multiple expression polymorphisms, suggesting trans-acting alleles with widespread transcriptional effects. Here, we have illustrated that cDNA-AFLP constitutes a powerful transcript profiling method that can be utilized for 'multifactorial genomics' analysis of any plant or animal species for which segregating populations and molecular marker maps are available.
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Affiliation(s)
- Marnik Vuylsteke
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B9052 Gent, Belgium.
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59
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Microspore gene expression associated with cytoplasmic male sterility and fertility restoration in sorghum. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s00497-005-0019-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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60
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Traas J, Bohn-Courseau I. Cell proliferation patterns at the shoot apical meristem. CURRENT OPINION IN PLANT BIOLOGY 2005; 8:587-92. [PMID: 16182603 DOI: 10.1016/j.pbi.2005.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 09/12/2005] [Indexed: 05/04/2023]
Abstract
The highly stereotypic cell proliferation patterns in many plant species suggest that the strict control of the cell cycle in time and space is an essential basis for ordered development. At the same time, conflicting evidence contradicts this view, indicating that cell division simply follows growth patterns that are dictated by the local availability of nutrients. Recent evidence shows that there is no strict hierarchical relationship between growth and proliferation. Cell expansion and proliferation, for example, are controlled by the same regulators. Cell proliferation depends on nutrient distribution but, in turn, the use of the same nutrients depends on the activity of cell cycle regulators such as E2F transcription factors.
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Affiliation(s)
- Jan Traas
- Institut National de la Recherche Agronomique (INRA), Laboratoire de Biologie Cellulaire, Route de Saint Cyr, 78026 Versailles cedex, France.
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61
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Blanco F, Garretón V, Frey N, Dominguez C, Pérez-Acle T, Van der Straeten D, Jordana X, Holuigue L. Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis. PLANT MOLECULAR BIOLOGY 2005; 59:927-44. [PMID: 16307367 DOI: 10.1007/s11103-005-2227-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 08/17/2005] [Indexed: 05/05/2023]
Abstract
Salicylic acid (SA) plays a crucial role in stress resistance in plants by modifying the expression of a battery of genes. In this paper, we report the identification of a group of early SA-regulated genes of Arabidopsis (activated between 0.5-2.5 h), using the cDNA-amplified fragment length polymorphism technique (cDNA-AFLP). Using 128 different primer combinations, we identified several genes based on their differential expression during SA treatment. Among these, we identified 12 genes up-regulated by SA whose patterns of induction were confirmed by Northern analysis. The identified genes can be grouped into two functional groups: Group 1: genes involved in cell protection (i.e. glycosyltransferases, glutathion S-transferases), and Group 2: genes involved in signal transduction (protein kinases and transcription factors). We also evaluated NPR1 requirement for the induction of the 12 up-regulated genes, and found that only those belonging to Group 2 require this co-activator for their expression. In silico analysis of the promoter sequences of the up-regulated genes, allowed us to identify putative cis-elements over-represented in these genes. Interestingly, as-1-like elements, previously characterized as SA-responsive elements, were specifically over-represented in Group 1 genes. The identification of early SA-regulated genes is an important step towards understanding the complex role of this hormone in plant stress resistance.
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Affiliation(s)
- Francisca Blanco
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, P.O. Box 114-D, Santiago, Chile
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62
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Fusco N, Micheletto L, Dal Corso G, Borgato L, Furini A. Identification of cadmium-regulated genes by cDNA-AFLP in the heavy metal accumulator Brassica juncea L. JOURNAL OF EXPERIMENTAL BOTANY 2005; 56:3017-27. [PMID: 16216843 DOI: 10.1093/jxb/eri299] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this study, cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis was employed to identify genes that exhibited a modulated expression following cadmium (Cd) treatment in Brassica juncea grown in hydroponic culture. Plants were treated for 6 h, 24 h, and 6 weeks with 10 microM Cd(NO3)2 and untreated 6-week-old plants were used as controls. Cd content was measured at these four time points. Long exposure to Cd affected root morphology: roots appeared thinner and sent out side roots. Seventy-three transcript-derived fragments were identified as Cd responsive. Fifty-two of them showed significant homology to genes with known or putative function, 10 transcript-derived fragments were homologous to uncharacterized genes, while 11 transcript-derived fragments did not show significant matches. The expression pattern of several of these genes was confirmed by northern blot analysis. Fifty-two genes of known or putative function were transcriptional factors, expression regulators, and stress responding and transport facilitation genes, as well as genes involved in cellular metabolism and organization and the photosynthetic process, suggesting that a multitude of processes are implicated in Cd stress response. The transcription of drought- and abscisic acid-responsive genes observed in this study also suggested that Cd imposes water stress and that abscisic acid may be involved in the Cd plant response.
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Affiliation(s)
- Nicola Fusco
- University of Verona, Department of Science and Technology, Strada le Grazie 15, I-37134 Verona, Italy
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63
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Nelissen H, Fleury D, Bruno L, Robles P, De Veylder L, Traas J, Micol JL, Van Montagu M, Inzé D, Van Lijsebettens M. The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth. Proc Natl Acad Sci U S A 2005; 102:7754-9. [PMID: 15894610 PMCID: PMC1140448 DOI: 10.1073/pnas.0502600102] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The key enzyme for transcription of protein-encoding genes in eukaryotes is RNA polymerase II (RNAPII). The recruitment of this enzyme during transcription initiation and its passage along the template during transcription elongation is regulated through the association and dissociation of several complexes. Elongator is a histone acetyl transferase complex, consisting of six subunits (ELP1-ELP6), that copurifies with the elongating RNAPII in yeast and humans. We demonstrate that point mutations in three Arabidopsis thaliana genes, encoding homologs of the yeast Elongator subunits ELP1, ELP3 (histone acetyl transferase), and ELP4 are responsible for the phenotypes of the elongata2 (elo2), elo3, and elo1 mutants, respectively. The elo mutants are characterized by narrow leaves and reduced root growth that results from a decreased cell division rate. Morphological and molecular phenotypes show that the ELONGATA (ELO) genes function in the same biological process and the epistatic interactions between the ELO genes can be explained by the model of complex formation in yeast. Furthermore, the plant Elongator complex is genetically positioned in the process of RNAPII-mediated transcription downstream of Mediator. Our data indicate that the Elongator complex is evolutionarily conserved in structure and function but reveal that the mechanism by which it stimulates cell proliferation is different in yeast and plants.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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64
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Kwade Z, Swiatek A, Azmi A, Goossens A, Inzé D, Van Onckelen H, Roef L. Identification of four adenosine kinase isoforms in tobacco By-2 cells and their putative role in the cell cycle-regulated cytokinin metabolism. J Biol Chem 2005; 280:17512-9. [PMID: 15731114 DOI: 10.1074/jbc.m411428200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenosine kinase (ADK), a key enzyme in the regulation of the intracellular level of adenosine is also speculated to be responsible for the conversion of cytokinin ribosides to their respective nucleotides. To elucidate the role of ADK in the cytokinin metabolism of tobacco BY-2 cells (Nicotiana tabacum cv. "Bright Yellow-2"; TBY-2), we have identified and characterized the full-length cDNAs encoding four ADK isoforms of N. tabacum and determined their catalytic properties. The four TBY-2 ADK isoforms (designated 1S, 2S, 1T, and 2T) display a high affinity for both adenosine (Km 1.88-7.30 microm) and three distinct types of cytokinin ribosides: isopentenyladenosine; zeatin riboside; and dihydrozeatin riboside (Km 0.30-8.71 microm). The Vmax/Km values suggest that ADK2S exhibits in vitro an overall higher efficiency in the metabolism of cytokinin ribosides than the other three isoforms. The expression pattern of NtADK genes is modulated significantly during the cell cycle. We suggest that the increased transcript accumulation of NtADK coupled to an increased ADK activity just prior to mitosis is associated with a very active cytokinin metabolism at that phase of the cell cycle of synchronized TBY-2 cells.
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Affiliation(s)
- Zuzanna Kwade
- Laboratory of Plant Biochemistry and Physiology, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
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65
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Kivioja T, Arvas M, Saloheimo M, Penttilä M, Ukkonen E. Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinformatics 2005; 21:2573-9. [PMID: 15774551 DOI: 10.1093/bioinformatics/bti393] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION cDNA amplified fragment length polymorphism (cDNA-AFLP) is one of the few genome-wide level expression profiling methods capable of finding genes that have not yet been cloned or even predicted from sequence but have interesting expression patterns under the studied conditions. In cDNA-AFLP, a complex cDNA mixture is divided into small subsets using restriction enzymes and selective PCR. A large cDNA-AFLP experiment can require a substantial amount of resources, such as hundreds of PCR amplifications and gel electrophoresis runs, followed by manual cutting of a large number of bands from the gels. Our aim was to test whether this workload can be reduced by rational design of the experiment. RESULTS We used the available genomic sequence information to optimize cDNA-AFLP experiments beforehand so that as many transcripts as possible could be profiled with a given amount of resources. Optimization of the selection of both restriction enzymes and selective primers for cDNA-AFLP experiments has not been performed previously. The in silico tests performed suggest that substantial amounts of resources can be saved by the optimization of cDNA-AFLP experiments.
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Affiliation(s)
- Teemu Kivioja
- Department of Computer Science, University of Helsinki, Helsinki, PO Box 68, FIN-00014, Finland.
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66
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Van Damme D, Bouget FY, Van Poucke K, Inzé D, Geelen D. Molecular dissection of plant cytokinesis and phragmoplast structure: a survey of GFP-tagged proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 40:386-98. [PMID: 15469496 DOI: 10.1111/j.1365-313x.2004.02222.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To identify molecular players implicated in cytokinesis and division plane determination, the Arabidopsis thaliana genome was explored for potential cytokinesis genes. More than 100 open reading frames were selected based on similarity to yeast and animal cytokinesis genes, cytoskeleton and polarity genes, and Nicotiana tabacum genes showing cell cycle-controlled expression. The subcellular localization of these proteins was determined by means of GFP tagging in tobacco Bright Yellow-2 cells and Arabidopsis plants. Detailed confocal microscopy identified 15 proteins targeted to distinct regions of the phragmoplast and the cell plate. EB1- and MAP65-like proteins were associated with the plus-end, the minus-end, or along the entire length of microtubules. The actin-binding protein myosin, the kinase Aurora, and a novel cell cycle protein designated T22, accumulated preferentially at the midline. EB1 and Aurora, in addition to other regulatory proteins (homologs of Mob1, Sid1, and Sid2), were targeted to the nucleus, suggesting that this organelle operates as a coordinating hub for cytokinesis.
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Affiliation(s)
- Daniël Van Damme
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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67
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Honys D, Twell D. Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol 2004; 5:R85. [PMID: 15535861 PMCID: PMC545776 DOI: 10.1186/gb-2004-5-11-r85] [Citation(s) in RCA: 541] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 09/17/2004] [Accepted: 09/28/2004] [Indexed: 12/12/2022] Open
Abstract
A transcriptome analysis of male gametophyte development in Arabidopsis uncovers distinct temporal classes of gene expression and opens the door to detailed studies of the regulatory pathways involved. Background The haploid male gametophyte generation of flowering plants consists of two- or three-celled pollen grains. This functional specialization is thought to be a key factor in the evolutionary success of flowering plants. Moreover, pollen ontogeny is also an attractive model in which to dissect cellular networks that control cell growth, asymmetric cell division and cellular differentiation. Our objective, and an essential step towards the detailed understanding of these processes, was to comprehensively define the male haploid transcriptome throughout development. Results We have developed staged spore isolation procedures for Arabidopsis and used Affymetrix ATH1 genome arrays to identify a total of 13,977 male gametophyte-expressed mRNAs, 9.7% of which were male-gametophyte-specific. The transition from bicellular to tricellular pollen was accompanied by a decline in the number of diverse mRNA species and an increase in the proportion of male gametophyte-specific transcripts. Expression profiles of regulatory proteins and distinct clusters of coexpressed genes were identified that could correspond to components of gametophytic regulatory networks. Moreover, integration of transcriptome and experimental data revealed the early synthesis of translation factors and their requirement to support pollen tube growth. Conclusions The progression from proliferating microspores to terminally differentiated pollen is characterized by large-scale repression of early program genes and the activation of a unique late gene-expression program in maturing pollen. These data provide a quantum increase in knowledge concerning gametophytic transcription and lay the foundations for new genomic-led studies of the regulatory networks and cellular functions that operate to specify male gametophyte development.
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Affiliation(s)
- David Honys
- Institute of Experimental Botany AS CR, Rozvojová 135, CZ-165 02, Praha 6, Czech Republic
- Department of Plant Physiology, Faculty of Sciences, Charles University, Viničná 5, CZ-128 44, Praha 2, Czech Republic
| | - David Twell
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
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Boudolf V, Vlieghe K, Beemster GTS, Magyar Z, Torres Acosta JA, Maes S, Van Der Schueren E, Inzé D, De Veylder L. The plant-specific cyclin-dependent kinase CDKB1;1 and transcription factor E2Fa-DPa control the balance of mitotically dividing and endoreduplicating cells in Arabidopsis. THE PLANT CELL 2004; 16:2683-92. [PMID: 15377755 PMCID: PMC520964 DOI: 10.1105/tpc.104.024398] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Accepted: 08/03/2004] [Indexed: 05/17/2023]
Abstract
Transgenic Arabidopsis thaliana plants overproducing the E2Fa-DPa transcription factor have two distinct cell-specific phenotypes: some cells divide ectopically and others are stimulated to endocycle. The decision of cells to undergo extra mitotic divisions has been postulated to depend on the presence of a mitosis-inducing factor (MIF). Plants possess a unique class of cyclin-dependent kinases (CDKs; B-type) for which no ortholog is found in other kingdoms. The peak of CDKB1;1 activity around the G2-M boundary suggested that it might be part of the MIF. Plants that overexpressed a dominant negative allele of CDKB1;1 underwent enhanced endoreduplication, demonstrating that CDKB1;1 activity was required to inhibit the endocycle. Moreover, when the mutant CDKB1;1 allele was overexpressed in an E2Fa-DPa-overproducing background, it enhanced the endoreduplication phenotype, whereas the extra mitotic cell divisions normally induced by E2Fa-DPa were repressed. Surprisingly, CDKB1;1 transcription was controlled by the E2F pathway, as shown by its upregulation in E2Fa-DPa-overproducing plants and mutational analysis of the E2F binding site in the CDKB1;1 promoter. These findings illustrate a cross talking mechanism between the G1-S and G2-M transition points.
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Affiliation(s)
- Véronique Boudolf
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Gent, Belgium
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69
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Rohde A, Morreel K, Ralph J, Goeminne G, Hostyn V, De Rycke R, Kushnir S, Van Doorsselaere J, Joseleau JP, Vuylsteke M, Van Driessche G, Van Beeumen J, Messens E, Boerjan W. Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. THE PLANT CELL 2004; 16:2749-71. [PMID: 15377757 PMCID: PMC520969 DOI: 10.1105/tpc.104.023705] [Citation(s) in RCA: 280] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Accepted: 07/14/2004] [Indexed: 05/17/2023]
Abstract
The first enzyme of the phenylpropanoid pathway, Phe ammonia-lyase (PAL), is encoded by four genes in Arabidopsis thaliana. Whereas PAL function is well established in various plants, an insight into the functional significance of individual gene family members is lacking. We show that in the absence of clear phenotypic alterations in the Arabidopsis pal1 and pal2 single mutants and with limited phenotypic alterations in the pal1 pal2 double mutant, significant modifications occur in the transcriptome and metabolome of the pal mutants. The disruption of PAL led to transcriptomic adaptation of components of the phenylpropanoid biosynthesis, carbohydrate metabolism, and amino acid metabolism, revealing complex interactions at the level of gene expression between these pathways. Corresponding biochemical changes included a decrease in the three major flavonol glycosides, glycosylated vanillic acid, scopolin, and two novel feruloyl malates coupled to coniferyl alcohol. Moreover, Phe overaccumulated in the double mutant, and the levels of many other amino acids were significantly imbalanced. The lignin content was significantly reduced, and the syringyl/guaiacyl ratio of lignin monomers had increased. Together, from the molecular phenotype, common and specific functions of PAL1 and PAL2 are delineated, and PAL1 is qualified as being more important for the generation of phenylpropanoids.
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Affiliation(s)
- Antje Rohde
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Ghent, Belgium
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70
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Matsuoka K, Demura T, Galis I, Horiguchi T, Sasaki M, Tashiro G, Fukuda H. A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. PLANT & CELL PHYSIOLOGY 2004; 45:1280-9. [PMID: 15509851 DOI: 10.1093/pcp/pch155] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
To understand how plant cell changes gene expression during cell division and after termination of cell division, we analyzed the change of gene expression during the growth of tobacco BY-2 cell lines using a cDNA microarray, which contained about 9,200 expression sequence tag fragments and corresponded to about 7,000 genes. We found that log phase cells predominantly expressed DNA/chromosome duplication gene homologs. In addition, many genes for basic transcription and translation machineries, as well as proteasomal genes, were up-regulated at the log phase. About half of the kinesin homolog genes, but not myosin homolog genes, were predominantly expressed at the dividing phase as well. In contrast, stationary phase cells expressed genes for many receptor kinases, signal transduction machineries and transcription factors. Several hundreds of genes showed differential expression after incubation of stationary phase cells with medium containing either salicylic acid or abscisic acid. These findings suggested that BY-2 cells at the stationary phase express genes for perceiving extracellular signals.
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Affiliation(s)
- Ken Matsuoka
- Plant Science Center, RIKEN (Institute of Physical and Chemical Research), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.
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71
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Schrader J, Nilsson J, Mellerowicz E, Berglund A, Nilsson P, Hertzberg M, Sandberg G. A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. THE PLANT CELL 2004; 16:2278-92. [PMID: 15316113 PMCID: PMC520933 DOI: 10.1105/tpc.104.024190] [Citation(s) in RCA: 260] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2004] [Accepted: 06/30/2004] [Indexed: 05/17/2023]
Abstract
Plant growth is the result of cell proliferation in meristems, which requires a careful balance between the formation of new tissue and the maintenance of a set of undifferentiated stem cells. Recent studies have provided important information on several genetic networks responsible for stem cell maintenance and regulation of cell differentiation in the apical meristems of shoots and roots. Nothing, however, is known about the regulatory networks in secondary meristems like the vascular cambium of trees. We have made use of the large size and highly regular layered organization of the cambial meristem to create a high-resolution transcriptional map covering 220 microm of the cambial region of aspen (Populus tremula). Clusters of differentially expressed genes revealed substantial differences in the transcriptomes of the six anatomically homogenous cell layers in the meristem zone. Based on transcriptional and anatomical data, we present a model for the position of the stem cells and the proliferating mother cells in the cambial zone. We also provide sets of marker genes for different stages of xylem and phloem differentiation and identify potential regulators of cambial meristem activity. Interestingly, analysis of known regulators of apical meristem development indicates substantial similarity in regulatory networks between primary and secondary meristems.
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Affiliation(s)
- Jarmo Schrader
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
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72
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De Paepe A, Vuylsteke M, Van Hummelen P, Zabeau M, Van Der Straeten D. Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 39:537-59. [PMID: 15272873 DOI: 10.1111/j.1365-313x.2004.02156.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A comprehensive transcriptome analysis by means of cDNA-amplified fragment length polymorphism (AFLP) and cDNA-microarray technology was performed in order to gain further understanding of the molecular mechanisms of immediate transcriptional response to ethylene. Col-0 plants were treated with exogenous ethylene and sampled at six different time-points ranging from 10 min until 6 h. In order to isolate truly ethylene-responsive genes, both the ethylene-insensitive mutant ein2-1 and the constitutive mutant (ctr1-1) were analysed in parallel by cDNA-AFLP while ein2-1 was included for the microarray experiment. Out of the cDNA-transcript profiling covering about 5% of the Arabidopsis transcriptome, 46 ethylene-responsive genes were isolated, falling in different classes of expression pattern and including a number of novel genes. Out of the 6008 genes present on the chip, 214 genes were significantly (alpha = 0.001) differentially expressed between Col-0 and ein2-1 over time. Cluster analysis and functional grouping of co-regulated genes allowed to determine the major ethylene-regulated classes of genes. In particular, a large number of genes involved in cell rescue, disease and defence mechanisms were identified as early ethylene-regulated genes. Furthermore, the data provide insight into the role of protein degradation in ethylene signalling and ethylene-regulated transcription and protein fate. Novel interactions between ethylene response and responses to several other signals have been identified by this study. Of particular interest is the overlap between ethylene response and responses to abscisic acid, sugar and auxin. In conclusion, the data provide unique insight into early regulatory steps of ethylene response.
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Affiliation(s)
- Annelies De Paepe
- Unit Plant Hormone Signalling and Bio-imaging, Department of Molecular Genetics, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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73
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Araki S, Ito M, Soyano T, Nishihama R, Machida Y. Mitotic cyclins stimulate the activity of c-Myb-like factors for transactivation of G2/M phase-specific genes in tobacco. J Biol Chem 2004; 279:32979-88. [PMID: 15175336 DOI: 10.1074/jbc.m403171200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myb transcription factors, which contain three imperfect repeats in the Myb domain, are evolutionarily conserved members of the Myb superfamily. Vertebrate Myb proteins with three repeats, c-Myb, A-Myb, and BMyb, play important roles at the G(1)/S transition in the cell cycle. In plants, this type of Myb protein controls the G(2)/M phase by activating or repressing the transcription of cyclin B genes and a variety of other G(2)/M phase-specific genes. In tobacco, two genes for Myb activators, NtmybA1 and NtmybA2, are transcriptionally controlled and are expressed specifically at the G(2)/M phase. As we showed here, in addition to the control at the transcriptional level, activity of NtmybA2 is also controlled at the post-translational level. We found that the transactivation potential of NtmybA2 is repressed by a regulatory domain located at its carboxyl terminus and that specific classes of cyclins A and B enhanced NtmybA2 activity possibly by relieving this inhibitory effect. Mutations at the 20 potential sites of phosphorylation by cyclin-dependent kinase (CDK) in NtmybA2 blocked the enhancing effects of the cyclins on NtmybA2 activity. Recombinant NtmybA2 was phosphorylated in vitro by a CDK fraction prepared from tobacco BY2 cells. The kinase activity for NtmybA2 in the CDK fraction was cell cycle-regulated in BY2 cells, peaking at the G(2)/M phase when the level of transcripts of cyclin B is maximal. Taken together, our data suggest that NtmybA2 is phosphorylated by a specific cyclin/CDK complex(es) at G(2)/M and that this phosphorylation removes the inhibitory effect of its C-terminal region, thereby activating NtmybA2 specifically at G(2)/M.
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Affiliation(s)
- Satoshi Araki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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74
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Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, DePamphilis CW, Ma H. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. PLANT PHYSIOLOGY 2004; 135:1084-99. [PMID: 15208425 PMCID: PMC514142 DOI: 10.1104/pp.104.040436] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Revised: 04/06/2004] [Accepted: 04/06/2004] [Indexed: 05/17/2023]
Abstract
Cyclins are primary regulators of the activity of cyclin-dependent kinases, which are known to play critical roles in controlling eukaryotic cell cycle progression. While there has been extensive research on cell cycle mechanisms and cyclin function in animals and yeasts, only a small number of plant cyclins have been characterized functionally. In this paper, we describe an exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants. Based on phylogenetic analysis, we define 10 classes of plant cyclins, four of which are plant-specific, and a fifth is shared between plants and protists but not animals. Microarray and reverse transcriptase-polymerase chain reaction analyses further provide expression profiles of cyclin genes in different tissues of wild-type Arabidopsis plants. Comparative phylogenetic studies of 174 plant cyclins were also performed. The phylogenetic results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals. Expression patterns and phylogenetic analyses of Arabidopsis cyclin genes suggest potential gene redundancy among members belonging to the same group. We discuss possible divergence and conservation of some plant cyclins. Our study provides an opportunity to rapidly assess the position of plant cyclin genes in terms of evolution and classification, serving as a guide for further functional study of plant cyclins.
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Affiliation(s)
- Guanfang Wang
- Department of Biology and the Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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75
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Boudolf V, Barrôco R, Engler JDA, Verkest A, Beeckman T, Naudts M, Inzé D, De Veylder L. B1-type cyclin-dependent kinases are essential for the formation of stomatal complexes in Arabidopsis thaliana. THE PLANT CELL 2004; 16:945-55. [PMID: 15031414 PMCID: PMC412868 DOI: 10.1105/tpc.021774] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Accepted: 02/13/2004] [Indexed: 05/17/2023]
Abstract
Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In yeasts, only one CDK is sufficient to drive cells through the cell cycle, whereas higher eukaryotes developed a family of related CDKs. Curiously, plants contain a unique class of CDKs (B-type CDKs), whose function is still unclear. We show that the CDKB1;1 gene of Arabidopsis (Arabidopsis thaliana) is highly expressed in guard cells and stomatal precursor cells of cotyledons, suggesting a prominent role for B-type CDKs in stomatal development. In accordance, transgenic Arabidopsis plants with reduced B-type CDK activity had a decreased stomatal index because of an early block of meristemoid division and inhibition of satellite meristemoid formation. Many aberrant stomatal cells were observed, all of them blocked in the G2 phase of the cell cycle. Although division of stomatal precursors was inhibited, cells still acquired stomatal identity, illustrating that stomatal cell differentiation is independent of cellular and nuclear division.
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Affiliation(s)
- Véronique Boudolf
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Gent, Belgium
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76
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Laukens K, Deckers P, Esmans E, Van Onckelen H, Witters E. Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture. Proteomics 2004; 4:720-7. [PMID: 14997494 DOI: 10.1002/pmic.200300614] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2003] [Indexed: 11/11/2022]
Abstract
Using two-dimensional gel electrophoresis (2-DE) and electrospray-tandem mass spectrometry (ESI-MS/MS), we have started the proteome analysis of the cell line Nicotiana tabacum cv. Bright Yellow-2 (tobacco BY-2). The BY-2 cell suspension culture is widely used as a model system to study the growth and development of plant cells. We present a protocol describing the sample preparation and 2-DE, enabling us to separate and display more than 1000 proteins from this cell culture. A reference gel was generated, using immobilized pH gradient isoelectric focusing in a linear gradient from pH 3 to 10 and 12% Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Although the tobacco genome is not sequenced yet, a range of protein spots from this reference map was identified by means of a semi-automated liquid chromatography-ESI-quadrupole time of flight-tandem MS (LC-ESI-QTOF-MS-MS) setup and cross-species matching. These data were integrated in a database, which can be accessed at http://tby2-www.uia.ac.be/tby2/. On the on-line reference map, the identified protein spots are hyperlinked to individual protein entries. Each protein entry contains all identification information, as well as links to relevant entries in other on-line databases. Comprehensive search functions are implemented. Especially for an unsequenced but widespread model organism like tobacco BY-2, such a reference database is a convenient source for protein information that brings protein identification within reach without the need for extensive MS. This publicly accessible database provides a solid basis for tobacco BY-2 proteomics in the future.
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Affiliation(s)
- Kris Laukens
- Laboratorium voor Planten-biochemie en -fysiologie, Department of Biology, University of Antwerp, Belgium.
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77
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Joubès J, De Schutter K, Verkest A, Inzé D, De Veylder L. Conditional, recombinase-mediated expression of genes in plant cell cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 37:889-96. [PMID: 14996220 DOI: 10.1111/j.1365-313x.2004.02004.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In plant cells, overexpression of critical genes can be hampered by deleterious effects on development that results in a counterselection of transgenic cells harboring the gene of interest. Inducible expression systems have been reported, but many of them show unwanted leaky expression. To circumvent this potential problem, a novel inducible system was developed based on two previously characterized systems: the CRE-loxP site-specific recombination system of bacteriophage P1 and the subcellular targeting of proteins by a mammalian glucocorticoid receptor (GR). By fusing the receptor domain of the rat GR to the carboxyl terminus of the CRE recombinase, a double-lock conditional transcriptional induction system was created that is highly useful to overexpress genes whose expression may block transgenic regeneration. Furthermore, because the designed vector utilizes the GATEWAY recombination technology, cloning was restriction- and ligation-free, thus rendering the vector suitable for high-throughput research. The system was tested in Nicotiana tabacum bright yellow-2 (BY-2) cells and its efficiency was demonstrated for the controlled overexpression of the gus reporter gene and a mutant allele of the A-type cyclin-dependent kinase (CDKA), which is known to be a potent inhibitor of the cell cycle.
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Affiliation(s)
- Jérôme Joubès
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Gent, Belgium
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78
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Lincker F, Philipps G, Chabouté ME. UV-C response of the ribonucleotide reductase large subunit involves both E2F-mediated gene transcriptional regulation and protein subcellular relocalization in tobacco cells. Nucleic Acids Res 2004; 32:1430-8. [PMID: 14990748 PMCID: PMC390297 DOI: 10.1093/nar/gkh310] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2004] [Revised: 02/05/2004] [Accepted: 02/05/2004] [Indexed: 12/22/2022] Open
Abstract
E2F factors are implicated in various cellular processes including specific gene induction at the G1/S transition of the cell cycle. We present in this study a novel regulatory aspect for the tobacco large subunit of ribonucleotide reductase (R1a) and its encoding gene (RNR1a) in the UV-C response. By structural analyses, two E2F sites were identified on the promoter of this gene. Functional analysis showed that, in addition to their role in the specific G1/S induction of the RNR1a gene, both E2F sites were important for regulating specific RNR1a gene expression in response to UV-C irradiation in non-synchronized and synchronized cells. Concomitantly, western blot and cellular analyses showed an increase of a 60 kDa E2F factor and a transient translocation of a GFP-R1a protein fusion from cytoplasm to nucleus in response to UV irradiation.
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Affiliation(s)
- Frédéric Lincker
- Institut de Biologie Moléculaire des Plantes du CNRS, Université Louis Pasteur, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
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79
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Vriezen WH, Achard P, Harberd NP, Van Der Straeten D. Ethylene-mediated enhancement of apical hook formation in etiolated Arabidopsis thaliana seedlings is gibberellin dependent. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 37:505-16. [PMID: 14756759 DOI: 10.1046/j.1365-313x.2003.01975.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Dark-grown Arabidopsis seedlings develop an apical hook by differential elongation and division of hypocotyl cells. This allows the curved hypocotyl to gently drag the apex, which is protected by the cotyledons, upwards through the soil. Several plant hormones are known to be involved in hook development, including ethylene, which causes exaggeration of the hook. We show that gibberellins (GAs) are also involved in this process. Inhibition of GA biosynthesis with paclobutrazol (PAC) prevented hook formation in wild-type (WT) seedlings and in constitutive ethylene response (ctr)1-1, a mutant that exhibits a constitutive ethylene response. In addition, a GA-deficient mutant (ga1-3) did not form an apical hook in the presence of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). Analysis of transgenic Arabidopsis seedlings expressing a green fluorescent protein (GFP)-repressor of ga1-3 (RGA) fusion protein suggested that ACC inhibits cell elongation in the apical hook by inhibition of GA signaling. A decreased feedback of GA possibly causes an induction of GA biosynthesis based upon the expression of genes encoding copalyl diphosphate synthase (CPS; GA1) and GA 2-oxidase (AtGA2ox1). Furthermore, expression of GASA1, a GA-response gene, suggests that differential cell elongation in the apical hook might be a result of differential GA-sensitivity.
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Affiliation(s)
- Wim H Vriezen
- Department of Molecular Genetics, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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80
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Grandjean O, Vernoux T, Laufs P, Belcram K, Mizukami Y, Traas J. In vivo analysis of cell division, cell growth, and differentiation at the shoot apical meristem in Arabidopsis. THE PLANT CELL 2004; 16:74-87. [PMID: 14671026 PMCID: PMC301396 DOI: 10.1105/tpc.017962] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Accepted: 10/21/2003] [Indexed: 05/18/2023]
Abstract
The aerial parts of the plant are generated by groups of rapidly dividing cells called shoot apical meristems. To analyze cell behavior in these structures, we developed a technique to visualize living shoot apical meristems using the confocal microscope. This method, combined with green fluorescent protein marker lines and vital stains, allows us to follow the dynamics of cell proliferation, cell expansion, and cell differentiation at the shoot apex. Using this approach, the effects of several mitotic drugs on meristem development were studied. Oryzalin (depolymerizing microtubules) very rapidly caused cell division arrest. Nevertheless, both cell expansion and cell differentiation proceeded in the treated meristems. Interestingly, DNA synthesis was not blocked, and the meristematic cells went through several rounds of endoreduplication in the presence of the drug. We next treated the meristems with two inhibitors of DNA synthesis, aphidicolin and hydroxyurea. In this case, cell growth and, later, cell differentiation were inhibited, suggesting an important role for DNA synthesis in growth and patterning.
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Affiliation(s)
- Olivier Grandjean
- Institut National de la Recherche Agronomique, Laboratoire Commun de Cytologie, Institut Jean-Pierre Bourgin, 78026 Versailles Cedex, France
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82
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Improvements of the Molecular Toolbox for Cell Cycle Studies in Tobacco BY-2 Cells. TOBACCO BY-2 CELLS 2004. [DOI: 10.1007/978-3-662-10572-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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83
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Polverari A, Molesini B, Pezzotti M, Buonaurio R, Marte M, Delledonne M. Nitric oxide-mediated transcriptional changes in Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:1094-105. [PMID: 14651343 DOI: 10.1094/mpmi.2003.16.12.1094] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nitric oxide (NO) is an essential regulatory molecule in several developmental processes and in the stress response in both animal and plant systems. Furthermore, key features of plant resistance to pathogens have been shown to depend on NO production, e.g., defense gene expression and the activation of a hypersensitive reaction (HR) in synergy with reactive oxygen species (ROS). Due to the many possible mechanisms of NO action, a clear picture of its involvement in plant resistance to pathogens is far from being achieved. Transcriptional changes related to NO action are likely to play a significant role in resistance and cell death. We investigated the changes in the expression profiles of Arabidopsis thaliana following infiltration with the NO donor sodium nitroprusside, by cDNA-amplification fragment length polymorphism (AFLP) transcript profiling. Altered expression patterns were detected for 120 of the approximately 2,500 cDNAs examined. Sequence analysis revealed homologies with genes involved in signal transduction, disease resistance and stress response, photosynthesis, cellular transport, and basic metabolism or with sequences coding for unknown proteins. Comparison of the expression profiles with data from public microarray sources revealed that many of the identified genes modulated by NO were previously reported to be modulated in disease-related experiments.
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Affiliation(s)
- Annalisa Polverari
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, 37134 Verona, Italy.
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84
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Abstract
Three decades have passed since the first recognition of restriction checkpoints in the plant cell cycle. Although many core cell cycle genes have been cloned, the mechanisms that control the G1-->S and G2-->M transitions in plants have only recently started to be understood. The cyclin-dependent kinases (CDKs) play a central role in the regulation of the cell cycle, and the activity of these kinases is steered by regulatory subunits, the cyclins. The activities of CDK-cyclin complexes are further controlled by an intricate panoply of monitoring mechanisms, which result in oscillating CDK activity during the division cycle. These fluctuations trigger transitions between the different stages of the cell cycle.
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Affiliation(s)
- Lieven De Veylder
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
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85
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Menges M, Hennig L, Gruissem W, Murray JAH. Genome-wide gene expression in an Arabidopsis cell suspension. PLANT MOLECULAR BIOLOGY 2003; 53:423-42. [PMID: 15010610 DOI: 10.1023/b:plan.0000019059.56489.ca] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant cell suspension cultures are invaluable models for the study of cellular processes. Here we develop the recently described Arabidopsis suspension culture MM2d as a transcript profiling platform by means of Affymetrix ATH1 microarrays. Analysis of gene expression profiles during normal culture growth, during synchronous cell cycle re-entry and during synchronous cell cycle progression provides a unique integrated view of gene expression responses in a higher-plant system. Particularly striking is that expression of over 14 000 genes belonging to all defined categories can be reliably detected, suggesting that integrated and comparative analysis of data sets derived from transcript profiling of cultures is a powerful approach to identify candidate components involved in a wide range of biological processes. Combinatorial analysis of independent cell cycle synchrony methods allows the identification of genes that are apparently cell-cycle-regulated but are most likely responding to the induction of synchrony. We thus present an integrated genome-wide view of the transcriptional profile of a plant suspension culture and identify a refined set of 1082 cell cycle regulated genes largely independent of synchrony method.
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Affiliation(s)
- Margit Menges
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
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86
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Vandenbussche F, Vriezen WH, Smalle J, Laarhoven LJJ, Harren FJM, Van Der Straeten D. Ethylene and auxin control the Arabidopsis response to decreased light intensity. PLANT PHYSIOLOGY 2003; 133:517-27. [PMID: 12972669 PMCID: PMC219028 DOI: 10.1104/pp.103.022665] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2003] [Revised: 04/14/2003] [Accepted: 06/30/2003] [Indexed: 05/18/2023]
Abstract
Morphological responses of plants to shading have long been studied as a function of light quality, in particular the ratio of red to far red light that affects phytochrome activity. However, changes in light quantity are also expected to be important for the shading response because plants have to adapt to the reduction in overall energy input. Here, we present data on the involvement of auxin and ethylene in the response to low light intensities. Decreased light intensities coincided with increased ethylene production in Arabidopsis rosettes. This response was rapid because the plants reacted within minutes. In addition, ethylene- and auxin-insensitive mutants are impaired in their reaction to shading, which is reflected by a defect in leaf elevation and an aberrant leaf biomass allocation. On the molecular level, several auxin-inducible genes are up-regulated in wild-type Arabidopsis in response to a reduction in light intensity, including the primary auxin response gene IAA3 and a protein with similarity to AUX22 and the 1-aminocyclopropane-1-carboxylic acid synthase genes ACS6, ACS8, and ACS9 that are involved in ethylene biosynthesis. Taken together, the data show that ethylene and auxin signaling are required for the response to low light intensities.
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87
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Goossens A, Häkkinen ST, Laakso I, Seppänen-Laakso T, Biondi S, De Sutter V, Lammertyn F, Nuutila AM, Söderlund H, Zabeau M, Inzé D, Oksman-Caldentey KM. A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc Natl Acad Sci U S A 2003; 100:8595-600. [PMID: 12826618 PMCID: PMC166274 DOI: 10.1073/pnas.1032967100] [Citation(s) in RCA: 313] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2002] [Indexed: 11/18/2022] Open
Abstract
Despite the tremendous importance of secondary metabolites for humans as for the plant itself, plant secondary metabolism remains poorly characterized. Here, we present an experimental approach, based on functional genomics, to facilitate gene discovery in plant secondary metabolism. Targeted metabolite analysis was combined with cDNA-amplified fragment length polymorphism-based transcript profiling of jasmonate-elicited tobacco Bright yellow 2 cells. Transcriptome analysis suggested an extensive jasmonate-mediated genetic reprogramming of metabolism, which correlated well with the observed shifts in the biosynthesis of the metabolites investigated. This method, which in addition to transcriptome data also generates gene tags, in the future might lead to the creation of novel tools for metabolic engineering of medicinal plant systems in general.
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Affiliation(s)
- Alain Goossens
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Suvi T. Häkkinen
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Into Laakso
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Tuulikki Seppänen-Laakso
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Stefania Biondi
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Valerie De Sutter
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Freya Lammertyn
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Anna Maria Nuutila
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Hans Söderlund
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Marc Zabeau
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Dirk Inzé
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Kirsi-Marja Oksman-Caldentey
- Department of Plant Systems Biology, Flanders
Interuniversity Institute for Biotechnology, Ghent University, K.L.
Ledeganckstraat 35, B-9000 Ghent, Belgium; VTT
Biotechnology, P.O. Box 1500 (Tietotie 2), FIN-02044 Espoo, Finland;
Department of Pharmacy, Division of
Pharmacognosy, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki,
Finland; and Dipartimento di Biologia,
Università di Bologna, Via Irnerio 42, I-40126 Bologna, Italy
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88
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Rombauts S, Florquin K, Lescot M, Marchal K, Rouzé P, van de Peer Y. Computational approaches to identify promoters and cis-regulatory elements in plant genomes. PLANT PHYSIOLOGY 2003; 132:1162-76. [PMID: 12857799 PMCID: PMC167057 DOI: 10.1104/pp.102.017715] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2002] [Revised: 01/10/2003] [Accepted: 03/17/2003] [Indexed: 05/19/2023]
Abstract
The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5'-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.
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Affiliation(s)
- Stephane Rombauts
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000 Gent, Belgium
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89
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Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, Inzé D, Zabeau M. Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics 2003; 269:173-9. [PMID: 12756529 DOI: 10.1007/s00438-003-0830-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2002] [Accepted: 02/05/2003] [Indexed: 11/25/2022]
Abstract
An improved cDNA-AFLP method for genome-wide expression analysis has been developed. We demonstrate that this method is an efficient tool for quantitative transcript profiling and a valid alternative to microarrays. Unique transcript tags, generated from reverse-transcribed messenger RNA by restriction enzymes, were screened through a series of selective PCR amplifications. Based on in silico analysis, an enzyme combination was chosen that ensures that at least 60% of all the mRNAs were represented by an informative sequence tag. The sensitivity and specificity of the method allows one to detect poorly expressed genes and distinguish between homologous sequences. Accurate gene expression profiles were determined by quantitative analysis of band intensities, and subtle differences in transcriptional activity were revealed. A detailed screen for cell cycle-modulated genes in tobacco demonstrates the usefulness of the technology for genome-wide expression analysis.
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Affiliation(s)
- P Breyne
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, Belgium
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90
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003; 4:277-84. [PMID: 18629117 PMCID: PMC2447404 DOI: 10.1002/cfg.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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