1
|
Pelletier G. Michel Caboche, an outstanding plant molecular and cell biologist. C R Biol 2021; 344:209-218. [DOI: 10.5802/crbiol.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022]
|
2
|
Roles of the transcriptional regulation mediated by the nitrate-responsive cis-element in higher plants. Biochem Biophys Res Commun 2011; 411:708-13. [DOI: 10.1016/j.bbrc.2011.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 07/02/2011] [Indexed: 11/24/2022]
|
3
|
Konishi M, Yanagisawa S. The regulatory region controlling the nitrate-responsive expression of a nitrate reductase gene, NIA1, in Arabidopsis. PLANT & CELL PHYSIOLOGY 2011; 52:824-36. [PMID: 21454300 DOI: 10.1093/pcp/pcr033] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nitrate reductase (NR) is the enzyme that catalyzes the first step of nitrate assimilation. It is well known that the expression of NR genes is rapidly induced in various plants by nitrate. Previously, the activity of a tobacco NR gene promoter was reported to be high in tobacco plants grown on medium containing ammonium as the sole nitrogen source, but low in tobacco plants grown on nitrate-containing medium. This cast some doubt on the role of the NR gene promoter in the nitrate-inducible expression of this gene. Furthermore, in previous studies, transformation with genomic fragments containing NR loci restored the reduced NR activity in NR mutants to a limited extent, suggesting a complex regulation of NR gene expression. Here, we show that although the 1.9 kb promoter of an NR gene in Arabidopsis, NIA1, is not activated by nitrate, the expression of a GUS (β-glucuronidase) reporter gene inserted between the 5'- and 3'-flanking sequences of the NIA1 coding region is strongly induced by nitrate. When the 3'-flanking sequence was fused downstream of the GUS gene under the control of the 35S minimal promoter, its expression was also strongly induced by nitrate. Furthermore, dissection analysis of the 3'-flanking region revealed that the sequence downstream of the transcriptional terminator rather than the 3'-untranslated region plays a role in nitrate-inducible expression, indicating a requirement for the 3'-flanking sequence for the nitrate-inducible transcription of NIA1. We also show that the 2.7 kb promoter sequence of NIA2, another NR gene of Arabidopsis, cannot direct nitrate-inducible expression.
Collapse
Affiliation(s)
- Mineko Konishi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | | |
Collapse
|
4
|
Feng H, Yan M, Fan X, Li B, Shen Q, Miller AJ, Xu G. Spatial expression and regulation of rice high-affinity nitrate transporters by nitrogen and carbon status. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:2319-32. [PMID: 21220781 DOI: 10.1093/jxb/erq403] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The high affinity nitrate transport system (HATS) plays an important role in rice nitrogen acquisition because, even under flooded anaerobic cultivation when NH(4)(+) dominates, significant nitrification occurs on the root surface. In the rice genome, four NRT2 and two NAR2 genes encoding HATS components have been identified. One gene OsNRT2.3 was mRNA spliced into OsNRT2.3a and OsNRT2.3b and OsNAR2.1 interacts with OsNRT2.1/2.2 and OsNRT2.3a to provide nitrate uptake. Using promoter-GUS reporter plants and semi-quantitative RT-PCR analyses, it was observed that OsNAR2.1 was expressed mainly in the root epidermal cells, differently from the five OsNRT2 genes. OsNAR2.1, OsNRT2.1, OsNRT2.2, and OsNRT2.3a were up-regulated by nitrate and suppressed by NH(4)(+) and high root temperature (37 °C). Expression of all these genes was increased by light or external sugar supply. Root transcripts of OsNRT2.3b and OsNRT2.4 were much less abundant and not affected by temperature. Expression of OsNRT2.3b was insensitive to the form of N supply. Expression of OsNRT2.4 responded to changes in auxin supply unlike all the other NRT2 genes. A region from position -311 to -1, relative to the translation start site in the promoter region of OsNAR2.1, was found to contain the cis-element(s) necessary for the nitrate-, but not light- and sugar-dependent activation. However, it was difficult to define a conserved cis-element in the promoters of the nitrate-regulated OsNRT2/OsNAR2 genes. The results imply distinct physiological functions for each OsNRT2 transporter, and differential regulation pathways by N and C status.
Collapse
Affiliation(s)
- Huimin Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
| | | | | | | | | | | | | |
Collapse
|
5
|
He P, Ma Y, Zhao G, Dai H, Li H, Chang L, Zhang Z. FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry. JOURNAL OF PLANT RESEARCH 2010; 123:707-14. [PMID: 20020171 DOI: 10.1007/s10265-009-0290-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 11/09/2009] [Indexed: 05/08/2023]
Abstract
Retrotransposons are ubiquitous in the plant kingdom and constitute a large fraction of many plant genomes. Although most retrotransposons from plants were thought to be transcriptionally silent in somatic tissues, evidence of activity under certain conditions is available in some cases. In this study, a complete LTR retrotransposon was isolated from the cultivated strawberry (Fragaria x ananassa) genome using genome walking. The element, named FaRE1, has all the features of a typical Ty1-copia retrotransposon. Its total length was 5,104 bp, comprising a single 3,891 bp open reading frame. It is represented by approximately 96 copies per genome, equivalent to approximately 0.33% of the genome. Transcription of FaRE1 was detected in leaf tissue treated with various phytohormones, such as naphthalene acetic acid, 2,4-dichlorophenoxyacetic acid or abscisic acid . To our knowledge, this is the first report of the isolation of a complete LTR retrotransposon with transcriptional activity in strawberry.
Collapse
Affiliation(s)
- Ping He
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
6
|
Konishi M, Yanagisawa S. Identification of a nitrate-responsive cis-element in the Arabidopsis NIR1 promoter defines the presence of multiple cis-regulatory elements for nitrogen response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:269-282. [PMID: 20444232 DOI: 10.1111/j.1365-313x.2010.04239.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nitrate is a major nitrogen source for land plants and also acts as a signaling molecule that induces changes in growth and gene expression. To identify the cis-acting DNA element involved in nitrate-responsive gene expression, we analyzed the promoter of the Arabidopsis gene encoding nitrite reductase (NIR1). A region from positions -188 to -1, relative to the translation start site, was found to contain at least one cis-element necessary for the nitrate-dependent activation of the promoter, in which the activity of nitrate transporter NRT2.1 and/or NRT2.2 plays a critical role. To define this nitrate-responsive cis-element (NRE), we compared the sequences of several nitrite reductase gene promoters from various higher plants and identified a conserved sequence motif as the putative NRE. A synthetic promoter in which the four copies of a 43-bp sequence containing the motif were fused to the 35S minimal promoter was found to direct nitrate-responsive transcription. Furthermore, mutations within this conserved motif in the native NIR1 promoter markedly reduced the nitrate-responsive activity of the promoter, indicating that the 43-bp sequence is an NRE that is both necessary and sufficient for nitrate-responsive transcription. We also show that both the native NIR1 promoter and the synthetic promoter display a similar level of sensitivity to nitrate, but respond differentially to exogenously supplied glutamine, indicating independent modulation of NIR1 expression by NRE-mediated nitrate induction and feedback repression mediated by other cis-element(s). These findings thus define the presence of multiple cis-elements involved in the nitrogen response in Arabidopsis.
Collapse
Affiliation(s)
- Mineko Konishi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Tiyoda-ku, Tokyo 102-8471, Japan
| | - Shuichi Yanagisawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- The Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan
| |
Collapse
|
7
|
Pathak RR, Das SK, Choudhury D, Raghuram N. Genomewide bioinformatic analysis negates any specific role for Dof, GATA and Ag/cTCA motifs in nitrate responsive gene expression in Arabidopsis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2009; 15:145-50. [PMID: 23572923 PMCID: PMC3550365 DOI: 10.1007/s12298-009-0016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nitrate response at the plant level is mediated by the transcriptional regulation of several hundreds of genes, but no common cis-acting nitrate-responsive elements (NREs) have been identified so far. Earlier, we bioinformatically ruled out the possibility that the previously published [(a/t)7Ag/cTCA] motif could act as NRE on its own (Das et al., 2007, Mol. Genet. Genomics, 278: 519-525). In the present study, we examined other motifs such as Dof and GATA binding elements in homologous as well as heterologous pairwise combinations in the Arabidopsis genome in silico. None of the above three motifs revealed any unique association with nitrate responsive genes or their subsets in any combination, either within their ORFs or 1 kb flanking sequences on either side. Additionally, twelve new, top-scoring candidate motifs that were generated using different online motif samplers were analyzed in silico using a subset of 21 'early' nitrate responsive genes, but did not reveal any specificity of occurence. These results underscore the need to continue the search for novel candidate NREs, as possible sites of intervention to understand/improve nitrate-responsive gene expression and nitrate use efficiency.
Collapse
Affiliation(s)
- Ravi Ramesh Pathak
- />School of Biotechnology, GGS Indraprastha University, Kashmiri Gate, Delhi, 110403 India
| | - Suman K. Das
- />School of Biotechnology, GGS Indraprastha University, Kashmiri Gate, Delhi, 110403 India
| | - Devapriya Choudhury
- />School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Nandula Raghuram
- />School of Biotechnology, GGS Indraprastha University, Kashmiri Gate, Delhi, 110403 India
| |
Collapse
|
8
|
Girin T, Lejay L, Wirth J, Widiez T, Palenchar PM, Nazoa P, Touraine B, Gojon A, Lepetit M. Identification of a 150 bp cis-acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant. PLANT, CELL & ENVIRONMENT 2007; 30:1366-80. [PMID: 17897408 DOI: 10.1111/j.1365-3040.2007.01712.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The Arabidopsis thaliana AtNRT2.1 gene, which encodes a NO(3)(-) transporter involved in high-affinity uptake by the roots, is a molecular target of several mechanisms responsible for the regulation of root NO(3)(-) acquisition by the N status of the plant. All levels of AtNRT2.1 expression (promoter activity, transcript level, protein accumulation, transport activity) are coordinately up-regulated in the presence of NO(3)(-), and repressed by downstream N metabolites. Transgenic plants expressing the GUS reporter gene under the control of upstream sequences of AtNRT2.1 have been studied to identify elements targeted by these two regulatory mechanisms. A 150 bp sequence located upstream of the TATA box that is required for both stimulation by NO(3)(-) and repression by N metabolites of the promoter has been identified. This sequence is able to confer these two regulations to a minimal promoter. Split-root experiments indicate that the stimulation of the chimaeric promoter by NO(3)(-) occurs only at the local level, whereas its repression by N metabolites is mediated by a systemic signal spread to the whole plant. The activity of the cis-acting 150 bp element is also regulated by sucrose supply to the roots, suggesting a possible interaction between N and C signalling within this short region. Accordingly, multiple motifs potentially involved in regulations by N and/or C status are identified within this sequence by bioinformatic approaches. This is the first report of such a cis-acting element in higher plants.
Collapse
Affiliation(s)
- Thomas Girin
- UMR 5004, Institut National de la Recherché Agronomique (INRA)--Centre National de la Recherche Scientifique (CNRS)-Sup Agro-UM2, Institut de Biologie Intégrative des Plantes, 2 Place Viala, Montpellier, F-34060 France
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Genomewide computational analysis of nitrate response elements in rice and Arabidopsis. Mol Genet Genomics 2007. [PMID: 17680272 DOI: 10.1007/s00438‐007‐0268‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Nitrate response element (NRE) was originally reported to be comprised of an Ag/cTCA core sequence motif preceded by a 7-bp AT rich region, based on promoter deletion analyses in nitrate and nitrite reductases from Arabidopsis thaliana and birch. In view of hundreds of new nitrate responsive genes discovered recently, we sought to computationally verify whether the above motif indeed qualifies to be the cis-acting NRE for all the responsive genes. We searched for the specific occurrence of at least two copies of the above motif in and around the nitrate responsive genes and elsewhere in the Arabidopsis and rice (Oryza sativa) genomes, with respect to their positional, orientational and strand-specific bias. This is the first comprehensive analysis of NREs for 625 nitrate responsive genes of Arabidopsis and their rice homologs, representing dicots and monocots, respectively. We report that the above motifs are present almost randomly throughout these genomes and do not reveal any specificity or bias towards nitrate responsive genes. This also seems to be true for smaller subsets of nitrate responsive genes in Arabidopsis, such as the 21 early responsive genes, 261 and 90 genes for root-specific and shoot-specific response, respectively, and 25 housekeeping genes. This necessitates a fresh search for candidate sequences that qualify to be NREs in these and other plants.
Collapse
|
10
|
Das SK, Pathak RR, Choudhury D, Raghuram N. Genomewide computational analysis of nitrate response elements in rice and Arabidopsis. Mol Genet Genomics 2007; 278:519-25. [PMID: 17680272 DOI: 10.1007/s00438-007-0268-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
Nitrate response element (NRE) was originally reported to be comprised of an Ag/cTCA core sequence motif preceded by a 7-bp AT rich region, based on promoter deletion analyses in nitrate and nitrite reductases from Arabidopsis thaliana and birch. In view of hundreds of new nitrate responsive genes discovered recently, we sought to computationally verify whether the above motif indeed qualifies to be the cis-acting NRE for all the responsive genes. We searched for the specific occurrence of at least two copies of the above motif in and around the nitrate responsive genes and elsewhere in the Arabidopsis and rice (Oryza sativa) genomes, with respect to their positional, orientational and strand-specific bias. This is the first comprehensive analysis of NREs for 625 nitrate responsive genes of Arabidopsis and their rice homologs, representing dicots and monocots, respectively. We report that the above motifs are present almost randomly throughout these genomes and do not reveal any specificity or bias towards nitrate responsive genes. This also seems to be true for smaller subsets of nitrate responsive genes in Arabidopsis, such as the 21 early responsive genes, 261 and 90 genes for root-specific and shoot-specific response, respectively, and 25 housekeeping genes. This necessitates a fresh search for candidate sequences that qualify to be NREs in these and other plants.
Collapse
Affiliation(s)
- Suman K Das
- School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmiri Gate, Delhi, 110 006, India
| | | | | | | |
Collapse
|
11
|
Lea US, Leydecker MT, Quilleré I, Meyer C, Lillo C. Posttranslational regulation of nitrate reductase strongly affects the levels of free amino acids and nitrate, whereas transcriptional regulation has only minor influence. PLANT PHYSIOLOGY 2006; 140:1085-94. [PMID: 16461378 PMCID: PMC1400556 DOI: 10.1104/pp.105.074633] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 01/07/2006] [Accepted: 01/09/2006] [Indexed: 05/06/2023]
Abstract
Diurnal variations in nitrate reductase (NR) activity and nitrogen metabolites were examined in wild-type Nicotiana plumbaginifolia and transformants with various degrees of NR deregulation. In the C1 line, NR was only deregulated at the transcriptional level by placing the NR gene under the control of the cauliflower mosaic virus 35S RNA promoter. In the Del8 and S521D lines, NR was additionally deregulated at the posttranslational level either by a deletion mutation in the N-terminal domain or by a mutation of the regulatory phosphorylation site (serine-521). Posttranslational regulation was essential for pronounced diurnal variations in NR activity. Low nitrate content was related to deregulation of NR, whereas the level of total free amino acids was much higher in plants with fully deregulated NR. Abolishing transcriptional and posttranslational regulation (S521D plants) resulted in an increase of glutamine and asparagine by a factor of 9 and 14, respectively, compared with wild type, whereas abolishing transcriptional regulation (C1 plants) only resulted in increases of glutamine and asparagine by factors <2. Among the minor amino acids, isoleucine and threonine, in particular, showed enhanced levels in S521D. Nitrate uptake rates were the same in S521D and wild type as determined with (15)N feeding. Deregulation of NR appears to set the level of certain amino acids, whereas diurnal variations were still determined by light/dark. Generally, deregulation of NR at the transcriptional level did not have much influence on metabolite levels, but additional deregulation at the posttranslational level resulted in profound changes of nitrogen metabolite levels.
Collapse
Affiliation(s)
- Unni S Lea
- Faculty of Science and Technology, University of Stavanger, Norway
| | | | | | | | | |
Collapse
|
12
|
Tapia G, Verdugo I, Yañez M, Ahumada I, Theoduloz C, Cordero C, Poblete F, González E, Ruiz-Lara S. Involvement of ethylene in stress-induced expression of the TLC1.1 retrotransposon from Lycopersicon chilense Dun. PLANT PHYSIOLOGY 2005; 138:2075-86. [PMID: 16040666 PMCID: PMC1183396 DOI: 10.1104/pp.105.059766] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The TLC1 family is one of the four families of long terminal repeat (LTR) retrotransposons identified in the genome of Lycopersicon chilense. Here, we show that this family of retroelements is transcriptionally active and its expression is induced in response to diverse stress conditions such as wounding, protoplast preparation, and high salt concentrations. Several stress-associated signaling molecules, including ethylene, methyl jasmonate, salicylic acid, and 2,4-dichlorophenoxyacetic acid, are capable of inducing TLC1 family expression in vivo. A representative of this family, named TLC1.1, was isolated from a genomic library from L. chilense. Transient expression assays in leaf protoplasts and stably transformed tobacco (Nicotiana tabacum) plants demonstrate that the U3 domain of the 5'-LTR region of this element can drive stress-induced transcriptional activation of the beta-glucuronidase reporter gene. Two 57-bp tandem repeated sequences are found in this region, including an 8-bp motif, ATTTCAAA, previously identified as an ethylene-responsive element box in the promoter region of ethylene-induced genes. Expression analysis of wild-type LTR and single and double ethylene-responsive element box mutants fused to the beta-glucuronidase gene shows that these elements are required for ethylene-responsive gene expression in protoplasts and transgenic plants. We suggest that ethylene-dependent signaling is the main signaling pathway involved in the regulation of the expression of the TLC1.1 element from L. chilense.
Collapse
Affiliation(s)
- Gerardo Tapia
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, Talca, Chile
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Lillo C, Meyer C, Ruoff P. The nitrate reductase circadian system. The central clock dogma contra multiple oscillatory feedback loops. PLANT PHYSIOLOGY 2001; 125:1554-7. [PMID: 11299336 PMCID: PMC1539380 DOI: 10.1104/pp.125.4.1554] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- C Lillo
- School of Technology and Science, Stavanger University College, Box 2557 Ullandhaug, N-4091 Stavanger, Norway.
| | | | | |
Collapse
|
14
|
Takeda S, Sugimoto K, Otsuki H, Hirochika H. A 13-bp cis-regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 18:383-93. [PMID: 10406122 DOI: 10.1046/j.1365-313x.1999.00460.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The tobacco Tto1 is one of the few active LTR-retrotransposons of plants, and its transposition is activated by tissue culture and is primarily regulated at the transcriptional level. The expression of Tto1 RNA can also be activated by various stresses, including viral infection, wounding, and treatment with jasmonate, a signal molecule of plant defence responses. It is shown here that the Tto1 LTR promoter is responsible for a high level of expression in cultured tissues of transgenic tobacco plants. We demonstrate that a 13-bp repeated motif (TGGTAGGTGAGAT) in the LTR functions as a cis-regulatory element, which confers the responsiveness to tissue culture, wounding and methyl jasmonate. Fungal elicitors also activate the promoter containing multiple copies of the 13-bp motif. Expression mediated by the 13-bp motif is activated markedly by okadaic acid and moderately by K252a, so that both phosphorylation and dephosphorylation of proteins are possibly involved in the signalling pathways. Interestingly, the 13-bp motif contains a conserved motif, Box L (also called AC-I or H-box like sequence) which has been shown to be involved in the expression of phenylpropanoid synthetic genes. Moreover, extended homologies are found between promoters of Tto1 and an asparagus defence gene, AoPR1, suggesting a possibility that the ancient insertion of an ancestral Tto1-related retrotransposon has provided some of the promoter/regulatory sequences, including the 13-bp motif-related sequence, of the AoPR1 gene. Based on the structural and functional similarity between the two promoters, a possible evolutionary role of the regulatory sequences of LTR-retrotransposons is discussed.
Collapse
Affiliation(s)
- S Takeda
- Department of Molecular Genetics, National Institute of Agrobiological Resources, Ibaraki, Japan
| | | | | | | |
Collapse
|
15
|
Yañez M, Verdugo I, Rodríguez M, Prat S, Ruiz-Lara S. Highly heterogeneous families of Ty1/copia retrotransposons in the Lycopersicon chilense genome. Gene 1998; 222:223-8. [PMID: 9831656 DOI: 10.1016/s0378-1119(98)00486-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have used the degenerated oligonucleotide primers-PCR (DOP-PCR) technique to determine the presence of Ty1/copia-related retrotransposons in the wild species of tomato, Lycopersicon chilense. Using degenerated oligonucleotides corresponding to highly conserved domains in the Ty1/copia retrotransposons, fragments of roughly 300 bp were obtained by PCR amplification. These were cloned in a plasmid vector and the nucleotide sequence determined for 20 clones, 19 of which showed sequence homology to retrotransposon-related sequences. Comparison of the deduced amino-acid sequence of these clones with those reported for other retrotransposons has allowed their classification into four distinct families: TLC1-TLC4. The level of amino-acid sequence similarity between these elements extends from 66.7% (between TLC1 and TLC2) to 42.6% (between TLC2 and TLC3). Altogether, the four families comprise about 0.17% of the L. chilense genome. RT-PCR analysis shows that the four TLC families are transcriptionally active, suggesting a mechanism for the generation of the observed diversity between the L. chilense retrotransposons.
Collapse
Affiliation(s)
- M Yañez
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, Casilla, 747, Talca, Chile
| | | | | | | | | |
Collapse
|
16
|
Meyer C, Pouteau S, Rouzé P, Caboche M. Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:194-200. [PMID: 8159170 DOI: 10.1007/bf00391013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.
Collapse
Affiliation(s)
- C Meyer
- Laboratoire de Biologie Cellulaire, INRA, Versailles, France
| | | | | | | |
Collapse
|
17
|
Grandbastien MA, Audeon C, Casacuberta JM, Grappin P, Lucas H, Moreau C, Pouteau S. Functional analysis of the tobacco Tnt1 retrotransposon. Genetica 1994; 93:181-9. [PMID: 7813914 DOI: 10.1007/bf01435250] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Retroelements represent by far the largest and most widespread class of mobile genetic elements. Representative of several classes of retrotransposons have been characterized in a broad range of plant species, but only a few of them have been shown to be active. Among these, the tobacco Tnt1 retrotransposon has been isolated after insertion mutagenesis and is one of the very few to be transcriptionally active. Tnt1 expression is strongly regulated in a tissue-specific and developmental manner. Moreover, Tnt1 expression is induced by a range of biotic or abiotic elicitors, which all have in common the ability to induce the plant defense response. Regulatory sequences involved in this elicitor-mediated induction have been located in the LTR U3 region. The link between Tnt1 activation and the plant defense response might represent an example of the involvement of transposable elements in genome restructurations needed in response to environmental fluctuations such as pathogen attacks.
Collapse
Affiliation(s)
- M A Grandbastien
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique--INRA, Cedex, France
| | | | | | | | | | | | | |
Collapse
|
18
|
Pilgrim ML, Caspar T, Quail PH, McClung CR. Circadian and light-regulated expression of nitrate reductase in Arabidopsis. PLANT MOLECULAR BIOLOGY 1993; 23:349-64. [PMID: 8219070 DOI: 10.1007/bf00029010] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The expression of a number of plant genes is regulated by an endogenous circadian clock. We report that the Arabidopsis NIA2 (nitrate reductase) gene shows robust circadian oscillations in mRNA accumulation which persist for at least 5 days in plants that have been grown in a light-dark (LD) cycle and then transformed to continuous light (LL). We further show that NIA2 mRNA accumulation oscillates in a circadian fashion in plants that have been grown in LD and then transferred to continuous darkness (DD). Results from nuclear run-on transcriptional analysis suggest that the oscillations in steady-state levels of NIA2 mRNA abundance are not primarily due to changes in transcription but, instead, reflect post-transcriptional regulation. The circadian oscillations in NIA2 mRNA abundance are paralleled by circadian oscillations in nitrate reductase enzyme activity (NR activity) in Arabidopsis plants that have been grown in LD and then transferred either to DD or to LL. Etiolated Arabidopsis seedlings express neither NIA2 mRNA nor NR activity. However, both NIA2 mRNA accumulation and NR activity are induced by exposure to white light. The inductive effects of light on NIA2 mRNA accumulation are due, at least in part, to a very low fluence phytochrome-mediated response. However, the persistence of circadian oscillations in NIA2 mRNA abundance for at least 5 days in LL demonstrates that the circadian clock is capable of overriding or gating the inductive effects of light on NIA2 mRNA accumulation in Arabidopsis for an extended, continuous period of time.
Collapse
Affiliation(s)
- M L Pilgrim
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755-3576
| | | | | | | |
Collapse
|
19
|
Daniel-Vedele F, Caboche M. A tobacco cDNA clone encoding a GATA-1 zinc finger protein homologous to regulators of nitrogen metabolism in fungi. MOLECULAR & GENERAL GENETICS : MGG 1993; 240:365-73. [PMID: 8413186 DOI: 10.1007/bf00280388] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In higher plants, the expression of the nitrate assimilation pathway is highly regulated. Although the molecular mechanisms involved in this regulation are currently being elucidated, very little is known about the trans-acting factors that allow expression of the nitrate and nitrite reductase genes which code for the first enzymes in the pathway. In the fungus Neurospora crassa, nit-2, the major nitrogen regulatory gene, activates the expression of unlinked structural genes that specify nitrogen-catabolic enzymes during conditions of nitrogen limitation. The nit-2 gene encodes a regulatory protein containing a single zinc finger motif defined by the C-X2-C-X17-C-X2-C sequence. This DNA-binding domain recognizes the promoter region of N. crassa nitrogen-related genes and fragments derived from the tomato nia gene promoter. The observed specificity of the binding suggests the existence of a NIT2-like homolog in higher plants. PCR and cross-hybridization techniques were used to isolate, respectively, a partial cDNA from Nicotiana plumbaginifolia and a full-length cDNA from Nicotiana tabacum. These clones encode a NIT2-like protein (named NTL1 for nit-2-like), characterized by a single zinc finger domain, defined by the C-X2-C-X18-C-X2-C amino acids, and associated with a basic region. The amino acid sequence of NTL1 is 60% homologous to the NIT2 sequence in the zinc finger domain. The Ntl1 gene is present as a unique copy in the diploid N. plumbaginifolia species. The characteristics of Ntl1 gene expression are compatible with those of a regulator of the nitrate assimilation pathway, namely weak nitrate inducibility and regulation by light.
Collapse
Affiliation(s)
- F Daniel-Vedele
- Laboratoire de Biologie Cellulaire, INRA, Versailles, France
| | | |
Collapse
|
20
|
Marion-Poll A, Marin E, Bonnefoy N, Pautot V. Transposition of the maize autonomous element Activator in transgenic Nicotiana plumbaginifolia plants. MOLECULAR & GENERAL GENETICS : MGG 1993; 238:209-17. [PMID: 8386800 DOI: 10.1007/bf00279549] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The maize autonomous transposable element Ac was introduced into haploid Nicotiana plumbaginifolia via Agrobacterium tumefaciens transformation of leaf disks. All the regenerated transformants (R0) were diploid and either homozygous or heterozygous for the hygromycin resistance gene used to select primary transformants. The Ac excision frequency was determined using the phenotypic assay of restoration of neomycin phosphotransferase activity and expression of kanamycin resistance among progeny seedlings. Some of the R0 plants segregated kanamycin-resistant seedlings in selfed progeny at a high frequency (34 to 100%) and contained one or more transposed Ac elements. In the primary transformants Ac transposition probably occurred during plant regeneration or early development. Other R0 transformants segregated kanamycin-resistant plants at a low frequency (< or = 4%). Two transformants of this latter class, containing a unique unexcised Ac element, were chosen for further study in the expectation that their kanamycin resistant progeny would result from independent germinal transposition events. Southern blot analysis of 32 kanamycin-resistant plants (R1 or R2), selected after respectively one or two selfings of these primary transformants, showed that 27 had a transposed Ac at a new location and 5 did not have any Ac element. Transposed Ac copy number varied from one to six and almost all transposition events were independent. Southern analysis of the R2 and R3 progeny of these kanamycin-resistant plants showed that Ac continued to transpose during four generations, and its activity increased with its copy number. The frequency of Ac transposition, from different loci, remained low (< or = 7%) from R0 to R3 generations when only one Ac copy was present.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- A Marion-Poll
- Laboratoire de Biologie Cellulaire, INRA, Versailles, France
| | | | | | | |
Collapse
|
21
|
Vincentz M, Moureaux T, Leydecker MT, Vaucheret H, Caboche M. Regulation of nitrate and nitrite reductase expression in Nicotiana plumbaginifolia leaves by nitrogen and carbon metabolites. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1993; 3:315-24. [PMID: 8220446 DOI: 10.1111/j.1365-313x.1993.tb00183.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nitrate (NR) and nitrite reductase (NiR) catalyse the reduction of nitrate to ammonium. The regulation of NR and NiR gene expression by carbohydrates (C) and nitrogen (N) metabolites was studied using detached leaves. In the dark, glucose fructose and sucrose supplied to detached green leaves of dark-adapted Nicotiana plumbaginifolia plants resulted in NR mRNA and protein accumulation and the loss of circadian rhythmicity in the size of the transcript pool. The characterization of transgenic plants expressing either a NR cDNA controlled by the 35S CaMV promoter or a transcriptional fusion between the tobacco nia1 (NR structural gene) promoter and the beta-glucuronidase reporter gene, led us to conclude that C metabolite control is taking place at the transcriptional level. Under low light conditions (limiting photosynthetic conditions), the supply of glutamine or glutamate resulted in a drop in the level of NR mRNA. Exogenously supplied carbohydrates partially antagonized this inhibitory effect suggesting that the availability of N and C metabolites affects the expression of the NR gene. The effects of carbohydrates and glutamine on NiR expression were also studied. NiR mRNA levels in the dark were relatively insensitive to feeding with glucose. Glutamate and glutamine were less efficient at decreasing NiR mRNA than NR mRNA levels. In contrast to NR, NiR mRNA levels were significantly increased by light treatments, indicating that NiR display regulatory characteristics reminiscent of photosynthetic genes such as the small subunit of ribulose bisphosphate carboxylase than to NR.
Collapse
Affiliation(s)
- M Vincentz
- Laboratoire de Biologie Cellulaire, INRA, Versailles, France
| | | | | | | | | |
Collapse
|