Nejvíce citovaný článek - PubMed ID 12519987
The effect of recalcitrant soil and water pollutant 2,4,6-trinitrotoluen (TNT) on gene expression in Arabidopsis thaliana rosettes and roots was studied separately for the first time using microarrays. Seven-day exposure to TNT resulted in 170 up- and 122 down-regulated genes in the rosettes and 61 up- and 51 down-regulated genes in the roots (expression difference > 1.5-fold; p[t test] < 0.05). TNT concentration, 5 µg/ml, was selected according to the dose response analysis and study of TNT uptake from liquid media. Although many TNT induced genes fell into ontology groups annotated as response to biotic and abiotic stresses in rosettes and roots, only a small overlap of TNT effects on transcriptome was observed between rosettes and roots. The rosettes exhibited induction of several genes associated with toxin metabolism, such as UDP-glycosyltransferases and ATP-binding cassette (ABC) family transporters. On the other side, no genes known to be involved in TNT transformation were found to be up-regulated in the roots. The genes coding for enzymes involved in the cell wall modifications were abundantly up-regulated in roots. Microarray data indicated that after a relatively long incubation with TNT (7 days), metabolism of this xenobiotic proceeded mainly in aerial parts, while its translocation into cell walls still took place in the roots. Results obtained by microarray hybridization were validated by quantitative real-time reverse-transcription PCR. Nitrate reductase 1, several glycosyltransferases and ABC transporters, sucrose-proton symporter 2, thioredoxin-dependent peroxidase 2, and gamma-glutamyltransferase are discussed for their potential to enhance detoxification and toleration capability of plants to TNT.
- MeSH
- Arabidopsis anatomie a histologie účinky léků metabolismus fyziologie MeSH
- membránové transportní proteiny genetika metabolismus MeSH
- metabolická inaktivace MeSH
- mikročipová analýza MeSH
- molekulární struktura MeSH
- proteiny huseníčku genetika metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- stanovení celkové genové exprese MeSH
- transferasy genetika metabolismus MeSH
- trinitrotoluen * farmakokinetika farmakologie MeSH
- výbušné látky farmakokinetika farmakologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- membránové transportní proteiny MeSH
- proteiny huseníčku MeSH
- transferasy MeSH
- trinitrotoluen * MeSH
- výbušné látky MeSH
BACKGROUND: Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures. RESULTS: The Rho GTPase-binding domain (GBD/FH3) reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm) formins that define a specific branch (Class III) of the formin family. CONCLUSION: We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored) Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms.
- MeSH
- fosfohydroláza PTEN genetika MeSH
- fylogeneze MeSH
- genetická variace MeSH
- Magnoliopsida enzymologie genetika MeSH
- molekulární evoluce * MeSH
- molekulární sekvence - údaje MeSH
- pravděpodobnostní funkce MeSH
- proteiny aktivující GTPasu genetika MeSH
- rho proteiny vázající GTP genetika MeSH
- rostlinné geny * MeSH
- rostlinné proteiny genetika MeSH
- sekvence aminokyselin MeSH
- sekvenční analýza proteinů MeSH
- sekvenční seřazení MeSH
- terciární struktura proteinů genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- fosfohydroláza PTEN MeSH
- proteiny aktivující GTPasu MeSH
- rho GTPase-activating protein MeSH Prohlížeč
- rho proteiny vázající GTP MeSH
- rostlinné proteiny MeSH
BACKGROUND: Microarray technologies now belong to the standard functional genomics toolbox and have undergone massive development leading to increased genome coverage, accuracy and reliability. The number of experiments exploiting microarray technology has markedly increased in recent years. In parallel with the rapid accumulation of transcriptomic data, on-line analysis tools are being introduced to simplify their use. Global statistical data analysis methods contribute to the development of overall concepts about gene expression patterns and to query and compose working hypotheses. More recently, these applications are being supplemented with more specialized products offering visualization and specific data mining tools. We present a curated gene family-oriented gene expression database, Arabidopsis Gene Family Profiler (aGFP; http://agfp.ueb.cas.cz), which gives the user access to a large collection of normalised Affymetrix ATH1 microarray datasets. The database currently contains NASC Array and AtGenExpress transcriptomic datasets for various tissues at different developmental stages of wild type plants gathered from nearly 350 gene chips. RESULTS: The Arabidopsis GFP database has been designed as an easy-to-use tool for users needing an easily accessible resource for expression data of single genes, pre-defined gene families or custom gene sets, with the further possibility of keyword search. Arabidopsis Gene Family Profiler presents a user-friendly web interface using both graphic and text output. Data are stored at the MySQL server and individual queries are created in PHP script. The most distinguishable features of Arabidopsis Gene Family Profiler database are: 1) the presentation of normalized datasets (Affymetrix MAS algorithm and calculation of model-based gene-expression values based on the Perfect Match-only model); 2) the choice between two different normalization algorithms (Affymetrix MAS4 or MAS5 algorithms); 3) an intuitive interface; 4) an interactive "virtual plant" visualizing the spatial and developmental expression profiles of both gene families and individual genes. CONCLUSION: Arabidopsis GFP gives users the possibility to analyze current Arabidopsis developmental transcriptomic data starting with simple global queries that can be expanded and further refined to visualize comparative and highly selective gene expression profiles.
