Refine
Year of publication
Is part of the Bibliography
- yes (49)
Keywords
- Quantitative Trait Locus (4)
- Quantitative Trait Locus analysis (4)
- recombinant inbred line (4)
- Arabidopsis thaliana (2)
- Partial Little Square (2)
- dominance effect (2)
- feature selection (2)
- recombinant inbred line population (2)
- Data standardisation and formatting (1)
- Experiment description (1)
- Experimental metadata (1)
- Hybrid prediction (1)
- LASSO (1)
- Maize (1)
- Minimum information recommendations (1)
- NF-X1 (1)
- Phenomics (1)
- Plant phenotyping (1)
- Regression (1)
- Solanaceae (1)
- Solanum lycopersicum (1)
- biological network (1)
- biomass (1)
- brassinosteroid (1)
- data standardisation and formatting (1)
- experiment description (1)
- experimental metadata (1)
- fruit (1)
- heterosis (1)
- metabolite profile (1)
- metabolite profiling (1)
- minimum information recommendations (1)
- molecular network (1)
- morphological analysis (1)
- partial correlation (1)
- plant phenotyping (1)
- primary metabolism (1)
- salt stress (1)
- seedlings (1)
- significant edge (1)
- tomato (1)
- transcript profiling (1)
The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative biolinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co- regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades
The comprehensive systems-biology database (CSB.DB) was used to reveal brassinosteroid (BR)-related genes from expression profiles based on co-response analyses. Genes exhibiting simultaneous changes in transcript levels are candidates of common transcriptional regulation. Combining numerous different experiments in data matrices allows ruling out outliers and conditional changes of transcript levels. CSB.DB was queried for transcriptional co-responses with the BR-signalling components BRI1 and BAK1: 301 out of 9694 genes represented in the nasc0271 database showed co-responses with both genes. As expected, these genes comprised pathway-involved genes (e.g. 72 BR-induced genes), because the BRI1 and BAK1 proteins are required for BR-responses. But transcript co-response takes the analysis a step further compared with direct approaches because BR-related non BR-responsive genes were identified. Insights into networks and the functional context of genes are provided, because factors determining expression patterns are reflected in correlations. Our findings demonstrate that transcript co-response analysis presents a valuable resource to uncover common regulatory patterns of genes. Different data matrices in CSB.DB allow examination of specific biological questions. All matrices are publicly available through CSB.DB. This work presents one possible roadmap to use the CSB.DB resources
In a screen for potential mediators of brassinosteroid (BR) effects, the EXORDIUM (EXO) protein was identified as a regulator of BR-responsive genes. The EXO gene was characterized as a BR-up-regulated gene. EXO overexpression under the control of the 35SCaMV promoter resulted in increased transcript levels of the BR-up-regulated KCS1, Exp5, delta-TIP, and AGP4 genes, which likely are involved in the mediation of BR-promoted growth. 35S::EXO lines grown in soil or in synthetic medium showed increased vegetative growth in comparison to wild-type plants, resembling the growth phenotype of BR-treated plants. Thus, the EXO protein most likely promotes growth via the modulation of gene expression patterns. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved
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
Heterosis has been widely used in agriculture to increase yield and to broaden adaptability of hybrid varieties and is applied to an increasing number of crop species. We performed a systematic survey of the extent and degree of heterosis for dry biomass in 63 Arabidopsis accessions crossed to three reference lines (Col-0, C24, and Nd). We detected a high heritability (69%) for biomass production in Arabidopsis. Among the 169 crosses analyzed, 29 exhibited significant mid-parent-heterosis for shoot biomass. Furthermore, we analyzed two divergent accessions, C24 and Col-0, the F-1 hybrids of which were shown to exhibit hybrid vigor, in more detail. In the combination Col-0/C24, heterosis for biomass was enhanced at higher light intensities; we found 51% to 66% mid-parent-heterosis at low and intermediate light intensities (60 and 120 mumol m(-2) s(-1)), and 161% at high light intensity (240 mumol m(-2) s(-1)). While at the low and intermediate light intensities relative growth rates of the hybrids were higher only in the early developmental phase (0-15 d after sowing [DAS]), at high light intensity the hybrids showed increased relative growth rates over the entire vegetative phase (until 25 DAS). An important finding was the early onset of heterosis for biomass; in the cross Col-0/C24, differences between parental and hybrid lines in leaf size and dry shoot mass could be detected as early as 10 DAS. The widespread occurrence of heterosis in the model plant Arabidopsis opens the possibility to investigate the genetic basis of this phenomenon using the tools of genetical genomics
Application of metabolomics to plant genotype discrimination using statistics and machine learning
(2003)
Stomatal cell biology
(2003)
The nuclear SHL protein is composed of a N-terminal BAH domain and a C-terminal PHD finger. Both domains are found in transcriptional regulators and chromatin-modifying proteins. Arabidopsis plants over-expressing SHL showed earlier flowering and senescence phenotype. To identify SHL regulated genes, expression profiles of 35S::SHL plants were established with Affymetrix ATH1 microarrays. About 130 genes showed reduced transcript levels, and about 45 genes showed increased transcript levels in 35S:: SHL plants. The up-regulated genes included AGL20 and AGL9, which most likely cause the early flowering phenotype of 35S:: SHL plants. Late-flowering SHL-antisense lines showed reduced AGL20 mRNA levels, suggesting that AGL20 gene expression depends on the SHL protein. The stronger expression of senescence- and defence-related genes (such as DIN2, DIN11 and PR-1) is in line with the early senescence phenotype of SHL-over- expressing plants. SHL-down-regulated genes included stress response genes and the PSR3.2 gene (encoding a beta- glucosidase). SHL over-expression did not alter the tissue specificity of PSR3.2 gene expression, but resulted in reduced transcript levels in both shoots and roots. Plants with glucocorticoid-inducible SHL over-expression were established and used for expression profiling as well. A subset of genes was identified, which showed consistent changes in the inducible system and in plants with constitutive SHL over-expression
Detailed analysis of brassinosteroid (BR)-regulated genes can provide evidence of the molecular basis of BR effects. Classical techniques (such as subtractive cDNA cloning) as well as cDNA and oligonucleotide microarrays have been applied to identify genes which are upregulated or downregulated after BR treatment or are differently expressed in BR-deficient or -insensitive mutants compared with wild type plants. Genes encoding cell-wall-modifying enzymes, enzymes of the BR biosynthetic pathway, auxin response factors, and transcription factors are subject to BR regulation. Effects on several other metabolic pathways and interactions with other phytohormones have been reported as well, although some of these effects may depend on certain environmental conditions (for example, light/dark or stress), the developmental stage of the plants, and tissue types. The identification of components of the BR signal transduction pathway revealed different modes of transcriptional control in animals and plants. Steroid signaling in plants comprises the plasma membrane receptor kinases BRI1 and BAK1 and intracellular protein phosphorylations. Thus, BR signaling in plants is reminiscent of growth factor and TGF-beta signal transduction in animals. The phosphorylation cascade could be a basis of extensive signaling cross-talk and thereby explain the complexity of BR responses