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T Altmann

Publications and source records attributed to T Altmann.

At least 19 recordsLinked to original sources
PubMed2003

Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis.

The major goal of this project was the establishment of a tool for rapid mapping of new mutations and genotyping in Arabidopsis consisting of at least 100 evenly spaced framework markers. We assembled a single nucleotide polymorphism (SNP)-based marker set consisting of 112 polymorphic sites with average spacing of 1.15 Mbp derived from an SNP database that we recently developed. This information was used to set up efficient SNP detection reactions based on multiplexed primer extension assays. The 112 Columbia (Col-0)/C24 framework markers were used to assemble 18 multiplexed SNaPshot assays with which up to eight separate loci can be genotyped in a single-tube/single-capillary format. In addition, for 110 framework markers matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) assays have been established for high throughput analyses. We demonstrated the usefulness and the robustness of both procedures of this tool by genotyping 48 BC3F1 individuals created between the accessions Col-0 and C24. Subsets of 10-62 of the established markers discriminate between various combinations of the accessions Col-0, C24, Landsberg erecta (Ler), Cape Verdi Islands (Cvi) and Niederzenz (Nd). Using a subset of 17 evenly distributed and established SNP markers that are also polymorphic between Ler and Col-0, we were able to rapidly map a mutant gene (tbr1) to an interval of 2.3 Mbp in an Ler (tbr1) x Col-0 cross.

Arabidopsis↗
PubMed2001

Integrated studies on plant biology using multiparallel techniques.

Plant biology, especially the fields of molecular genetics and molecular physiology, is currently undergoing a change in paradigm from 'vertical' analysis of the role(s) of one or a few genes to 'horizontal' holistic approaches, studying the function of many or even all of the genes of an organism simultaneously. This change is leading us beyond genomes to transcriptomes, proteomes and metabalomes, and to an understanding of life at an entirely new level. Profiling strategies are putting this change into effect through the generation of large amounts of data, requiring that current bioinformatic approaches adapt and grow in order to make the most of these data.

Arabidopsis↗
PubMed2001

Brassinosteroid signaling in plants.

In animals and humans, steroid hormones (SHs) regulate gene transcription via the binding of nuclear receptors. In addition, rapid nongenomic effects of steroids occur and appear to be mediated by plasma-membrane receptors. Plants also use steroids as signaling molecules. These brassinosteroids (BRs) show structural similarity to the SHs of vertebrates and insects. Plant mutants defective in brassinosteroid biosynthesis or perception exhibit dwarfism and reduced fertility, and reveal the need for BRs during growth and development. BR signaling in Arabidopsis thaliana and rice (Oryza sativa) - dicotyledonous and monocotyledonous models, respectively - is mediated by the receptor kinases BRI1 and OsBRI1. The extracellular domain of BRI1 perceives BRs and the signal is mediated via an intracellular kinase domain that autophosphorylates Ser and Thr residues and apparently has the potential to phosphorylate other substrates. BRI1 transduces steroid signals across the plasma membrane and mediates genomic effects.

Arabidopsis↗
PubMed2001

Stomatal cell biology.

In the past two years, major advances in our knowledge of the cellular events involved in the formation of stomatal complexes, particularly those responsible for the establishment of the stomatal pattern, have been made. These events are altered in the Arabidopsis mutants sdd1-1, tmm and flp. Molecular cloning of the SDD1 gene initiated the elucidation of the underlying molecular mechanisms. The proposed function of SDD1 as a processing protease provides a hint towards the involvement of a proteinaceous signal in the formation of stomatal complexes.

Arabidopsis↗
PubMed2001

Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis.

Gene expression in response to Fe deficiency was analyzed in Arabidopsis roots and shoots through the use of a cDNA collection representing at least 6,000 individual gene sequences. Arabidopsis seedlings were grown 1, 3, and 7 d in the absence of Fe, and gene expression in roots and shoots was investigated. Following confirmation of data and normalization methods, expression of several sequences encoding enzymes known to be affected by Fe deficiency was investigated by microarray analysis. Confirmation of literature reports, particularly for changes in enzyme activity, was not always possible, but changes in gene expression could be confirmed. An expression analysis of genes in glycolysis, the tricarboxylic acid cycle, and oxidative pentose phosphate pathway revealed an induction of several enzymes within 3 d of Fe-deficient growth, indicating an increase in respiration in response to Fe deficiency. In roots, transcription of sequences corresponding to enzymes of anaerobic respiration was also induced, whereas in shoots, the induction of several genes in gluconeogenesis, starch degradation, and phloem loading was observed. Thus, it seemed likely that the energy demand in roots required for the Fe deficiency response exceeded the capacity of oxidative phosphorylation, and an increase in carbon import and anaerobic respiration were required to maintain metabolism.

Adaptation, Physiological↗
PubMed2000

A subtilisin-like serine protease involved in the regulation of stomatal density and distribution in Arabidopsis thaliana.

Stomata are specialized cellular structures in the epidermis of aerial plant organs that control gas exchange (H(2)O release and CO(2) uptake) between leaves and the atmosphere by modulating the aperture of a pore flanked by two guard cells. Stomata are nonrandomly distributed, and their density is controlled by endogenous and environmental factors. To gain insight into the molecular mechanisms regulating stomatal distribution, Arabidopsis thaliana mutants with altered stomatal characteristics were isolated and examined. The sdd1-1 mutant exhibits a two- to fourfold increase of stomatal density and formation of clustered stomata (i.e., stomata that are not separated by intervening pavement cells), whereas the internal leaf architecture is not altered. The SDD1 gene was identified by map-based cloning. It encodes a subtilisin-like serine protease related to prokaryotic and eukaryotic proteins. We propose that SDD1 acts as a processing protease involved in the mediation of a signal that controls the development of cell lineages that lead to guard cell formation.

Amino Acid Sequence↗
PubMed2000

12-Oxophytodienoate reductase 3 (OPR3) is the isoenzyme involved in jasmonate biosynthesis.

In addition to OPR1 and OPR2, two isoenzymes of 12-oxophytodienoate reductase, a third isoform (OPR3) has recently been identified in Arabidopsis thaliana (L.) Heynh. The expression of the OPR3 gene is induced not only by a variety of stimuli, such as touch, wind, wounding, UV-light and application of detergent, but also by brassinosteroids. The three enzymes were expressed in a functional form in Escherichia coli, and OPR2 was additionally expressed in insect cell cultures and overexpressed in A. thaliana. Substrate conversion was analyzed using a stereospecific assay. The results show that OPR3 effectively converts the natural (9S,13S)-12-oxophytodienoic acid [Km = 35 microM, Vmax 53.7 nkat (mg protein)-1] to the corresponding 3-2(2'(Z)-pentenyl) cyclopentane-1-octanoic acid (OPC-8:0) stereoisomer while OPR1 and OPR2 convert (9S,13S)-12-oxophytodienoic acid with greatly reduced efficiency compared to OPR3. Thus, OPR3 is the isoenzyme relevant for jasmonate biosynthesis.

Arabidopsis↗
PubMed2000

The Arabidopsis PHD-finger protein SHL is required for proper development and fertility.

The SHL gene from Arabidopsis thaliana encodes a small nuclear protein that contains a BAH domain and a PHD finger. Both domains are found in numerous (putative) transcriptional regulators and chromatin-remodeling factors. Different sets of transgenic lines were established to analyze the physiological relevance of SHL. SHL expression driven by the CaMV 35S promoter results in reduced growth, early flowering, early senescence, and impaired flower and seed formation. Antisense inhibition of SHL expression gives rise to dwarfism and delayed development. In-frame N-terminal fusion of the SHL protein to beta-glucuronidase (GUS) directs GUS to the nucleus of stably transformed Arabidopsis plants. Thus, SHL encodes a novel putative regulator of gene expression, which directly or indirectly influences a broad range of developmental processes.

Amino Acid Sequence↗
PubMed2000

Metabolite profiling for plant functional genomics.

Multiparallel analyses of mRNA and proteins are central to today's functional genomics initiatives. We describe here the use of metabolite profiling as a new tool for a comparative display of gene function. It has the potential not only to provide deeper insight into complex regulatory processes but also to determine phenotype directly. Using gas chromatography/mass spectrometry (GC/MS), we automatically quantified 326 distinct compounds from Arabidopsis thaliana leaf extracts. It was possible to assign a chemical structure to approximately half of these compounds. Comparison of four Arabidopsis genotypes (two homozygous ecotypes and a mutant of each ecotype) showed that each genotype possesses a distinct metabolic profile. Data mining tools such as principal component analysis enabled the assignment of "metabolic phenotypes" using these large data sets. The metabolic phenotypes of the two ecotypes were more divergent than were the metabolic phenotypes of the single-loci mutant and their parental ecotypes. These results demonstrate the use of metabolite profiling as a tool to significantly extend and enhance the power of existing functional genomics approaches.

Arabidopsis↗
PubMed2000

Analysis of phosphate acquisition efficiency in different Arabidopsis accessions.

The morphological and physiological characteristics of Arabidopsis accessions differing in their phosphate acquisition efficiencies (PAEs) when grown on a sparingly soluble phosphate source (hydroxylapatite) were analyzed. A set of 36 accessions was subjected to an initial PAE evaluation following cultivation on synthetic, agarose-solidified media containing potassium phosphate (soluble) or hydroxylapatite (sparingly soluble). From the five most divergent accessions identified in this way, C24, Co, and Cal exhibited high PAEs, whereas Col-0 and Te exhibited low PAEs. These five accessions were analyzed in detail. Significant differences were found in root morphology, phosphate uptake kinetics, organic acid release, rhizosphere acidification, and the ability of roots to penetrate substrates. Long root hairs at high densities, high uptake per unit root length, and high substrate penetration ability in the efficient accessions C24 and Co mediate their high PAEs. The third accession with high PAE, Cal, exhibits a high shoot-to-root ratio, long roots with long root hairs, and rhizosphere acidification. These results are consistent with previous observations and highlight the suitability of using Arabidopsis accessions to identify and isolate genes determining the PAE in plants.

Arabidopsis↗
PubMed1999

Molecular cloning and expression analyses of mitochondrial and plastidic isoforms of cysteine synthase (O-acetylserine(thiol)lyase) from Arabidopsis thaliana.

Cysteine synthase, the key enzyme for fixation of inorganic sulfide, catalyses the formation of cysteine from O-acetylserine and inorganic sulfide. Here we report the cloning of cDNAs encoding cysteine synthase isoforms from Arabidopsis thaliana. The isolated cDNA clones encode for a mitochondrial and a plastidic isoform of cysteine synthase (O-acetylserine (thiol)-lyase, EC 4.2.99.8), designated cysteine synthase C (AtCS-C, CSase C) and B (AtCS-B; CSase B), respectively. AtCS-C and AtCS-B, having lengths of 1569-bp and 1421-bp, respectively, encode polypeptides of 430 amino acids (approximately 45.8 kD) and of 392 amino acids (approximately 41.8 kD), respectively. The deduced amino acid sequences of the mitochondrial and plastidic isoforms exhibit high homology even with respect to the presequences. The predicted presequence of AtCS-C has a N-terminal extension of 33 amino acids when compared to the plastidic isoform. Northern blot analysis showed that AtCS-C is higher expressed in roots than in leaves whereas the expression of AtCS-B is stronger in leaves. Furthermore, gene expression of both genes was enhanced by sulfur limitation which in turn led to an increase in enzyme activity in crude extracts of plants. Expression of the AtCS-B gene is regulated by light. The mitochondrial, plastidic and cytosolic (Hesse and Altmann, 1995) isoforms of cysteine synthase of Arabidopsis are able to complement a cysteine synthase-deficient mutant of Escherichia coli unable to grow on minimal medium without cysteine, indicating synthesis of functional plant proteins in the bacterium. Two lines of evidence proved that AtCS-C encodes a mitochondrial form of cysteine synthase; first, import of in vitro translation products derived from AtCS-C in isolated intact mitochondria and second, Western blot analysis of mitochondria isolated from transgenic tobacco plants expressing AtCS-C cDNA/c-myc DNA fusion protein.

Amino Acid Sequence↗
PubMed1999

Hypoxia during early developmental period induces long-term changes in the dopamine content and release in a mesencephalic cell culture.

The present study was conducted to elucidate the long-term effects of exposure to hypoxia of dopaminergic neurons during the early developmental period. Primary mesencephalic cell cultures prepared from fetal rats and containing 0.5-2% of dopaminergic neurons were exposed to hypoxia between in vitro days 1 and 6, the putative critical developmental period. Changes in the content, release and uptake of dopamine were found to depend on the degree of hypoxia and on the duration of exposure. Following moderate hypoxia (7 h, 5% O2) on two consecutive days between in vitro days 1 and 3, the cultures showed a small increase in the dopamine levels, by 16%. After severe hypoxia (0% O2/95% N2 for 24 h), during the same time window, the cellular dopamine content was elevated by 100%. Moreover, severe hypoxia produced long-lasting modulations of the dopaminergic system. On in vitro day 14, cells exhibited increased levels of 3,4-dihydroxyphenylacetic acid and homovanillic acid (by 34% and 55%, respectively), and elevations of both the spontaneous and potassium-stimulated dopamine release by 70%. The dopamine transport and metabolism of cells exposed to hypoxia between in vitro days 4 and 6 remained unchanged with regard to long-term effects. The present study provides strong evidence for the induction of long-term changes in dopaminergic cells due to hypoxia during the critical developmental period in mesencephalic culture. The developmental period capable of inducing long-lasting changes in dopamine metabolism is restricted to in vitro days 1-3.

Animals↗
PubMed1999

A complete BAC-based physical map of the Arabidopsis thaliana genome.

Arabidopsis thaliana is a small flowering plant that serves as the major model system in plant molecular genetics. The efforts of many scientists have produced genetic maps that provide extensive coverage of the genome (http://genome-www. stanford.edu/Arabidopsis/maps.html). Recently, detailed YAC, BAC, P1 and cosmid-based physical maps (that is, representations of genomic regions as sets of overlapping clones of corresponding libraries) have been established that extend over wide genomic areas ranging from several hundreds of kilobases to entire chromosomes. These maps provide an entry to gain deeper insight into the A. thaliana genome structure. A. thaliana has been chosen as the subject of the first large-scale project intended to determine the full genome sequence of a plant. This sequencing project, together with the increasing interest in map-based gene cloning, has highlighted the requirement for a complete and accurate physical map of this plant species. To supply the scientific community with a high-quality resource, we present here a complete physical map of A. thaliana using essentially the IGF BAC library. The map consists of 27 contigs that cover the entire genome, except for the presumptive centromeric regions, nucleolar organization regions (NOR) and telomeric areas. This is the first reported map of a complex organism based entirely on BAC clones and it represents the most homogeneous and complete physical map established to date for any plant genome. Furthermore, the analysis performed here serves as a model for an efficient physical mapping procedure using BAC clones that can be applied to other complex genomes.

Arabidopsis↗
PubMed1998

Construction and characterization of the IGF Arabidopsis BAC library.

A bacterial artificial chromosome (BAC) library has been established for Arabidopsis thaliana (ecotype Col-0) covering about seven haploid nuclear genome equivalents. This library, called the Institut für Genbiologische Forschung (IGF) BAC library, consists of 10,752 recombinant clones carrying inserts (generated by partial EcoRI digestion) of an average size of about 100 kb in a modified BAC vector, pBeloBAC-Kan. Hybridization with organellar DNA and nuclear repetitive DNA elements revealed the presence of 1.1% clones with mitochondrial DNA, 0.2% clones with plastid DNA, 3.2% clones with the 180 bp paracentromeric repeat, 1.6% clones with 5S rDNA, and 10.8% clones with the 18S-25S rDNA repeat. With its extensive genome coverage, its rather uniformly sized inserts (80 kb < 85% < 120 kb) and low contamination with organellar DNA, this library provides an excellent resource for A. thaliana genomic mapping, map-based gene cloning, and genome sequencing.

Arabidopsis↗
PubMed1998

A tale of dwarfs and drugs: brassinosteroids to the rescue.

Brassinosteroids (BRs), a specific class of low abundance plant steroids, are capable of eliciting strong growth responses and a variety of physiological changes through exogenous application to plants. Recently, BRs gained general acceptance as important regulators (hormones) of plant growth and development through genetic and molecular identification and characterization of genes involved in BR biosynthesis or response in Arabidopsis, pea and tomato. This major advance in the molecular genetics of BR biosynthesis and mode of action disclosed another case of amazing functional conservation of signalling molecules utilized in plants and animals, and provided a set of extremely valuable tools for the functional analysis of BRs.

Mutation↗
PubMed1998

Recent advances in brassinosteroid molecular genetics.

The importance of brassinosteroids (BRs, a specific class of ecdysone-like plant steroids) as essential endogenous regulators of growth and development is demonstrated through a growing number of well characterised Arabidopsis, pea, and tomato mutants deficient in BR biosynthesis or BR response. Thus, a rapid advancement in understanding the molecular genetics of BR biosynthesis and mode of action can be witnessed, which will be further enhanced through the availability of a set of extremely valuable molecular tools for the analysis of the biological function of BRs.

Mutation↗