| 1. |
- Hilson, P., et al.
(författare)
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Versatile gene-specific sequence tags for Arabidopsis functional genomics : Trancript profiling and reverse genetics applications
- 2004
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 14:10B, s. 2176-2189
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Tidskriftsartikel (refereegranskat)abstract
- Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.
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| 2. |
- Boerjan, W., et al.
(författare)
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Superroot, a recessive mutation in Arabidopsis, confers auxin overproduction
- 1995
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Ingår i: The Plant Cell. - : JSTOR. - 1040-4651 .- 1532-298X. ; 7:9, s. 1405-1419
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Tidskriftsartikel (refereegranskat)abstract
- We have isolated seven allelic recessive Arabidopsis mutants, designated superroot (sur1-1 to sur1-7), displaying several abnormalities reminiscent of auxin effects. These characteristics include small and epinastic cotyledons, an elongated hypocotyl in which the connection between the stele and cortical and epidermal cells disintegrates, the development of excess adventitious and lateral roots, a reduced number of leaves, and the absence of an inflorescence. When germinated in the dark, sur1 mutants did not develop the apical hook characteristic of etiolated seedlings, We were able to phenocopy the Sur1(-) phenotype by supplying auxin to wild-type seedlings, to propagate sur7 explants on phytohormone-deficient medium, and to regenerate shoots from these explants by the addition of cytokinins alone to the culture medium. Analysis by gas chromatography coupled to mass spectrometry indicated increased levels of both free and conjugated indole-3-acetic acid. sur1 was crossed to the mutant axr2 and the altered-auxin response mutant ctr1. The phenotype of both double mutants was additive. The sur1 gene was mapped on chromosome 2 at 0.5 centimorgans from the gene encoding phytochrome B.
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| 3. |
- Creusot, F., et al.
(författare)
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The CIC YAC library: Sizing of the clones and determination of clones carrying repeated DNA sequences.
- 1995
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Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 8:5, s. 763-770
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Tidskriftsartikel (refereegranskat)abstract
- A new Arabidopsis thaliana (ecotype Columbia) genomic library has been constructed in Yeast Artificial Chromosomes: the CIC library (for CEPH, INRA and CNRS). Optimization of plant culture conditions and protoplast preparation allowed the recovery of large amounts of viable protoplasts. Mechanical shearing of DNA was minimized by isolation of DNA from protoplasts embedded in agarose. Cloning of large inserts was favored by including two successive size fractionation steps (after partial EcoRI digestion and after ligation with the vector arms), which selected DNA fragments larger than 350 kb. The library consists of 1152 clones with an average insert size of 420 kb. Clones carrying chloroplast DNA and various nuclear repeated sequences have been identified. Twenty-one per cent of the clones are found to contain chloroplast DNA. Therefore, the library represents around four nuclear genome equivalents. The clones containing 5S rDNA genes, 18S-25S rDNA sequences and the 180 bp paracentromeric repeated element account for 3.6%, 8.9% and 5.8%, respectively. Only one clone was found to carry the 160 bp paracentromeric repeated element. Given the smaller size of clones carrying Arabidopsis repeated DNA, the average size of remaining clones is around 480 kb. The library was screened by PCR amplification using pairs of primers corresponding to sequences dispersed in the genome. Seventy out of 76 pairs of primers identified from one to seven YAC clones. Thus at least 92% of the genome is represented in the CIC library. The survey of the library for clones containing unlinked DNA sequences indicates that the proportion of chimeric clones is lower than 10%.
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| 4. |
- Seo, M., et al.
(författare)
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Higher activity of an aldehyde oxidase in the auxin-overproducing superroot1 mutant of Arabidopsis thaliana
- 1998
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 116:2, s. 687-693
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Tidskriftsartikel (refereegranskat)abstract
- Aldehyde oxidase (AO; EC 1.2.3.1) activity was measured in seedlings of wild type or an auxin-overproducing mutant, superroot1 (sur1), of Arabidopsis thaliana. Activity staining for AO after native polyacrylamide gel electrophoresis separation of seedling extracts revealed that there were three major bands with AO activity (AO1-3) in wild-type and mutant seedlings. One of them (AO1) had a higher substrate preference for indole-3-aldehyde. This AO activity was significantly higher in sur1 mutant seedlings than in the wild type. The difference in activity was most apparent 7 d after germination, the same time required for the appearance of the remarkable sur1 phenotype, which includes epinastic cotyledons, elongated hypocotyls, and enhanced root development. Higher activity was observed in the root and hypocotyl region of the mutant seedlings. We also assayed the indole-3-acetaldehyde oxidase activity in extracts by high-performance liquid chromatography detection of indole-3-acetic acid (IAA). The activity was about 5 times higher in the extract of the sur1 seedlings, indicating that AO1 also has a substrate preference for abscisic aldehyde. Treatment of the wild-type seedlings with picloram or IAA caused no significant increase in AO1 activity. This result suggested that the higher activity of AO1 in sur1 mutant seedlings was not induced by IAA accumulation and, thus, strongly supports the possible role of AO1 in IAA biosynthesis in Arabidopsis seedlings.
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| 5. |
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| 6. |
- Delarue, M., et al.
(författare)
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cristal mutations in Arabidopsis confer a genetically heritable, recessive, hyperhydric phenotype
- 1997
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Ingår i: Planta. - : Springer Science and Business Media LLC. - 0032-0935 .- 1432-2048. ; 202:1, s. 51-61
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Tidskriftsartikel (refereegranskat)abstract
- A new class of recessive Arabidopsis mutants, designated cristal (cii) has been isolated which display several abnormalities reminiscent of hyperhydric symptoms. These characteristics include translucent and wrinkled cotyledons and leaves, abnormal chloroplast organization, a reduced amount of chlorophyll, a reduced dry weight and a decreased number of palisade cells in the leaves accompanied by an increase of intercellular space, and therefore give a vitreous appearance to the aerial part. The phenotype is also dependent on the culture medium water potential. The cril gene was mapped on chromosome 4 close to the DHS1 marker.
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| 7. |
- Delarue, M., et al.
(författare)
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Sur2 mutations of Arabidopsis thaliana define a new locus involved in the control of auxin homeostasis
- 1998
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Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 14:5, s. 603-611
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Tidskriftsartikel (refereegranskat)abstract
- A new auxin homeostasis gene in Arabidopsis called SUR2 has been identified. This gene, mapped to the bottom of chromosome 4, is defined by two recessive nuclear mutants designated superroot2 (sur2), which display several abnormalities reminiscent of auxin effects. A number of these characteristics are similar to the phenotype of the previously described auxin-overproducing mutant superroot1 (sur1); however, several lines of evidences reveal that the SUR2 gene defines a new key point in the regulation of endogenous auxin concentrations. The phenotype of the sur1 sur2 double mutant is additive. Analysis by gas chromatography coupled to mass spectrometry indicated increased levels of free indole-3-acetic acid correlated with a decreased level of bound auxin in the sur2 mutant. These results suggest that SUR2 may be involved in the control of auxin conjugation.
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| 8. |
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| 9. |
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| 10. |
- Santoni, V., et al.
(författare)
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A comparison or two-dimensional electrophoresis data with phenotypical traits in Arabidopsis leads to the identification of a mutant (cri1) that accumulates cytokinins
- 1997
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Ingår i: Planta. - : Springer Science and Business Media LLC. - 0032-0935 .- 1432-2048. ; 202:1, s. 62-69
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Tidskriftsartikel (refereegranskat)abstract
- Total proteins extracted from developmental mutants of Arabidopsis thaliana (L.) Heyhn, and from wild-type plants cultivated in the presence of various hormones were analyzed by two-dimensional (2-D) gel electrophoresis. Computer analysis of 2-D gels followed by a statistical treatment of data allowed us to build a phenogram that describes the biochemical distances between the different genotypes. Analysis of the 2-D electrophoresis data allowed us to discriminate mutants in agreement with phenotypical and physiological traits. This biochemical analysis helped us to develop a working hypothesis which led us to show that one developmental mutant (cril) overaccumulates cytokinins.
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| 11. |
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| 12. |
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| 13. |
- Bohmert, K., et al.
(författare)
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AGO1 defines a novel locus of Arabidopsis controlling leaf development
- 1998
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Ingår i: EMBO Journal. - : Wiley. - 0261-4189 .- 1460-2075. ; 17:1, s. 170-180
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Tidskriftsartikel (refereegranskat)abstract
- An allelic series of the novel argonaute mutant (ago1-1 to ago1-6) of the herbaceous plant Arabidopsis thaliana has been isolated, The ago1 mutation pleotropically affects general plant architecture, The apical shoot meristem generates rosette leaves and a single stem, but axillary meristems rarely develop, Rosette leaves lack a leaf blade but still show adaxial/abaxial differentiation, Instead of cauline leaves, filamentous structures without adaxial/abaxial differentiation develop along the stem and an abnormal inflorescence bearing infertile flowers with filamentous organs is produced, Two independent T-DNA insertions into the AGO1 locus led to the isolation of two corresponding genomic sequences as well as a complete cDNA. The AGO1 locus was mapped close to the marker mi291a on chromosome 1. Antisense expression of the cDNA resulted in a partial mutant phenotype, Sense expression caused some transgenic lines to develop goblet-like leaves and petals, The cDNA encodes a putative 115 kDa protein with sequence similarity tea translation products of a novel gene family present in nematodes as,yell as humans, No specific function has been assigned to these genes, Similar proteins are not encoded by the genomes of yeast or bacteria, suggesting that AGOI belongs to a novel class of genes with a function specific to multicellular organisms.
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| 14. |
- Cowling, R. J., et al.
(författare)
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The role of PASTICCINO1, an FKBP-like protein, in plant development
- 1999
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- The pasticcino (pas) mutants of Arabidopsis thaliana were identified due to their abnormal response to cytokinins. These mutants fall into 3 complementation groups: pas1 (2 alleles), pas2 (1 allele) and pas3 (4 alleles). The mutants all have excessive and disorganised cell divisions leading to extra cell layers in the hypocotyl, abnormal apical meristems, and rosettes with fused vitreous leaves. This cell proliferation effect is exaggerated in the presence of cytokinins. The PAS1 gene was cloned via a T-DNA insertion; it encodes for a protein with similarities to FK506-binding proteins (FKBPs), a class of immunophilins. Like other large FKBPs the PAS1 protein has several putative FKBP domains, a tetratricopeptide repeat domain and a calmodulin binding motif. PAS1 also has conserved nuclear localisation signals. Although the presence of immunophilins has been demonstrated in plants, their functions are unknown. PAS1 is the first plant immunophilin-like gene to be disrupted and suggests a role for PAS 1 in the control of plant cell division.
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| 15. |
- Desnos, T., et al.
(författare)
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Procuste1 mutants identify two distinct genetic pathways controlling hypocotyl cell elongation, respectively in dark and light-grown Arabidopsis seedlings
- 1996
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Ingår i: Development. - 0950-1991 .- 1477-9129. ; 122:2, s. 683-693
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Tidskriftsartikel (refereegranskat)abstract
- Plant morphogenesis is dependent on a tight control of cell division and expansion. Cell elongation during postembryonic hypocotyl growth is under the control of a light-regulated developmental switch. Light is generally believed to exert its effects on hypocotyl elongation through a phytochrome- and blue-light receptor- mediated inhibitory action on a so far unknown cell elongation mechanism. We describe here a new class of allelic mutants in Arabidopsis, at the locus PROCUSTE1 (prc1-1 to -4), which have a hypocotyl elongation defect specifically associated with the dark-grown developmental program. Normal hypocotyl elongation is restored in plants grown in white, blue or red light. In agreement with this, the constitutive photomorphogenic mutation cop1-6, which induces a deetiolated phenotype in the dark, is epistatic to prc1-2 for the hypocotyl phenotype. Epistasis analyses in red and blue light respectively, indicate that phytochrome B but not the blue light receptor HY4, is required for the switch from PRC1-dependent to PRC1-independent elongation. The conditional hypocotyl growth defect is associated with a deformation of the hypocotyl surface due to an uncontrolled swelling of epidermal, cortical or endodermal cells, suggesting a defect in the structure of the expanding cell wall, A similar phenotype was observed in elongating roots, which was however, independent of the light conditions. The aerial part of mature mutant plants grown in the light was indistinguishable from the wild type. prc1 mutants provide a means of distinguishing, for the first time, two genetic pathways regulating hypocotyl cell elongation respectively in dark- and light-grown seedlings, whereby light not only inhibits hypocotyl growth, but also activates a PRC1-independent cell elongation program.
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| 16. |
- Faure, J. D., et al.
(författare)
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The PASTICCINO genes of Arabidopsis thaliana are involved in the control of cell division and differentiation
- 1998
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Ingår i: Development. - 0950-1991 .- 1477-9129. ; 125:5, s. 909-918
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Tidskriftsartikel (refereegranskat)abstract
- The control of cell division by growth regulators is critical to proper plant development. The isolation of single-gene mutants altered in the response to plant hormones should permit the identification of essential genes controlling the growth and development of plants. We have isolated mutants pasticcino belonging to 3 complementation groups (pas1, pas2, pas3) in the progeny of independent ethyl methane sulfonate and T-DNA mutagenized Arabidopsis thaliana plants. The screen was performed in the presence or absence of cytokinin. The mutants isolated were those that showed a significant hypertrophy of their apical parts when grown on cytokinin-containing medium. The pas mutants have altered embryo, leaf and root development. They display uncoordinated cell divisions which are enhanced by cytokinin. Physiological and biochemical analyses show that cytokinins are probably involved in pas phenotypes. The PAS genes have been mapped respectively to chromosomes 3, 5 and 1 and represent new plant genes involved in the control of cell division and plant development.
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| 17. |
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| 18. |
- Santoni, V., et al.
(författare)
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Use of two-dimensional protein pattern analysis for the characterization of Arabidopsis thaliana mutants.
- 1994
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Ingår i: Planta. - 0032-0935 .- 1432-2048. ; 192:4, s. 557-566
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Tidskriftsartikel (refereegranskat)abstract
- Total proteins extracted from wild-type plants of Arabidopsis thaliana Heyhn, an etiolated mutant, a de-etiolated mutant and a mutant affected in cotyledon morphology, were analyzed by two-dimensional gel electrophoresis. Computer analysis of two-dimensional gels allowed the characterization of the mutants by a set of proteins showing a differential expression when compared with the wild-type plant grown under the same conditions. The overlap between comparisons of the different mutants with the wild-type allowed the identification of groups of polypeptides which, since their expression is altered in several mutants, might be involved in certain physiological functions. For example, this approach showed a possible involvement of actin in the elongation process. The simultaneous analysis of the two-dimensional protein patterns of different mutants seems, therefore, to be a promising approach to characterize proteins involved in various physiological functions.
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| 19. |
- Traas, J., et al.
(författare)
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Normal Differentiation Pattern in Plants Lacking Microtubular Preprophase Bands
- 1995
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 375:6533, s. 676-677
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Tidskriftsartikel (refereegranskat)abstract
- IT is generally accepted that polarized cell expansion and the strict control of division plane alignment are prerequisites for ordered spatial development in higher plants(1). This appears to be linked to the presence of cell walls, which immobilize the cells and fix their relative positions. In this context, the cortical cytoskeleton is thought to play a central role(1-6). Interphase microtubules are often aligned perpendicular to the growth axis and it has been proposed that they control cell expansion, probably in combination with the cell wall. Another cytoskeletal array, the prephophase band, has been associated with division plane alignment. This structure, which girdles the cell at the G2 phase of the cell cycle and at prophase, precisely predicts the future division site and probably fixes it. Here we describe different mutants in Arabidopsis that are unable to form these two cortical microtubular arrays. As expected, this defect is associated with irregular cell expansion and the inability to align division planes. Surprisingly, however, the mutations do not affect differentiation patterns: all cell types and organs are in their correct relative positions.
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