Following completion of Arabidopsis thaliana sequencing projects, multiple resistance gene analogues (RGAs) have been identified. In this work a review of the current state of knowledge available in protein databases and scientific articles is presented. Putative resistance genes were identified by using BLAST searches as well as HMM fingerprints (the latter to infer existence of characteristic domains). The representation of all five classes of putative resistance genes in Col-0 ecotype was examined, along with the statistics on RGAs present on all five chromosomes of Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>The gene regulatory information is hardwired in the promoter regions formed by <it>cis</it>-regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fundamental to understanding gene expression. The determination of the regulatory circuits controlled by each TF and the identification of the <it>cis</it>-regulatory sequences for all genes have been identified as two of the goals of the Multinational Coordinated <it>Arabidopsis thaliana </it>Functional Genomics Project by the Multinational <it>Arabidopsis </it>Steering Committee (June 2002).</p> <p>Results</p> <p>AGRIS is an information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtTFDB (<it>Arabidopsis thaliana </it>transcription factor database) and AtcisDB (<it>Arabidopsis thaliana cis</it>-regulatory database). AtTFDB contains information on approximately 1,400 transcription factors identified through motif searches and grouped into 34 families. AtTFDB links the sequence of the transcription factors with available mutants and, when known, with the possible genes they may regulate. At<it>cis</it>DB consists of the 5' regulatory sequences of all 29,388 annotated genes with a description of the corresponding <it>cis</it>-regulatory elements. Users can search the databases for (i) promoter sequences, (ii) a transcription factor, (iii) a direct target genes for a specific transcription factor, or (vi) a regulatory network that consists of transcription factors and their target genes.</p> <p>Conclusion</p> <p>AGRIS provides the necessary software tools on <it>Arabidopsis </it>transcription factors and their putative binding sites on all genes to initiate the identification of transcriptional regulatory networks in the model dicotyledoneous plant <it>Arabidopsis thaliana</it>. AGRIS can be accessed from <url>http://arabidopsis.med.ohio-state.edu</url>.</p>

By inserting entomological needles into the lower parts of young inflorescence stems of three-month-old Arabidopsis thaliana (L.) Heynh var. Colombia plants, we studied the process of regenerative xylem production. Regenerative xylem was formed only in one- to two-day-old inflorescence stems but not in older ones. The regenerative vessels originated from re-differentiation of cortical parenchyma. To characterize the process of regenerative xylem formation, we conducted a histological study from the time of wounding to day 30 after wounding. In the first day after wounding the tissues showed no structural responses except for the wounding itself. After six days, regenerative vessel members were already differentiating in a basipetal pattern, forming a vascular bypass around the wound. Regenerative vessel member formation reached a maximal level on the twelfth day after wounding. Sixteen days after wounding the pith parenchyma started to become loose as if indicating tissue senescence. Altogether, vascular regeneration following wounding in inflorescence stems of Arabidopsis thaliana is similar to that in other dicotyledon plants. These findings provide the basis for the use of Arabidopsis thaliana as a model system to study the genetics, physiology and cell biology of wound healing and regenerative vascular tissue formation.

Seed of Arabidopsis thaliana accumulate carotenoids during development. These are mainly β-carotene, violaxanthin and lutein. By overexpression of an endogenous phytoene synthase (psy) under control of the seed-specific napin (nap) promoter the carotenoid content was elevated, resulting in increased levels in mainly β-carotene, violaxanthin, lutein and α-carotene. Transgenic seeds were also found to contain increased levels of ABA and displayed a delay in germination. The levels of ABA had a good correlation to the varying increases in lutein and violaxanthin content in seeds from plants hemizygous for the nap:psy construct. Seeds from plants overexpressing a β-carotene ketolase (bkt) from the green algae Haematococcus pluvialis, also under control of the napin promoter contained small amounts of ketocarotenoids, mainly 4-keto-lutein. When plants carrying the nap:bkt construct were crossed to plants carrying nap:psy this resulted in seeds where the total ketocarotenoid content had increased up to 13-fold. In seeds of the aba1-3 mutant of Arabidopsis which is mutated in the zeaxanthin epoxididase (zep) zeaxanthin levels were increased up to 40-fold and in seed of plants overexpressing an endogenous β-carotene hydroxylase (bch) it was found that the violaxanthin content had increased up to 20-fold. In seed from plants transgenic for nap:bch, neoxanthin and ABA levels were also increased. Just as for plants transgenic for nap:psy these seeds displayed a delay in germination. When γ-tocopherol content was analysed it was found that in seeds of nap:psy and nap:bch transformants it was only half of that found in wild type. In the Arabidopsis mutant abscisic acid-insensitive 3-1 (abi3-1) that is mutated in a seed-specific transcription factor, the seeds were found to have increased levels of β-carotene, violaxanthin, lutein and γ-tocopherol.

The shoot apical meristem of higher plants consists of a population of stem cells at the tip of the plant body that continuously gives rise to organs such as leaves and flowers. Cells that leave the meristem differentiate and must be replaced to maintain the integrity of the meristem. The balance between differentiation and maintenance is governed both by the environment and the developmental status of the plant. In order to respond to these different stimuli, the meristem has to be plastic thus ensuring the stereotypic shape of the plant body. Meristem plasticity requires the ZWILLE (ZLL) gene. In zll mutant embryos, the apical cells are misspecified causing a variability of the meristem’s size and function. Using specific antibodies against ZLL, we show that the zll phenotype is due to the complete absence of the ZLL protein. In immunohistochemical experiments we confirm the observation that ZLL is solely localized in vascular tissue. For a better understanding of the role of ZLL in meristem stability, we analysed the genetic interactions of ZLL with WUSCHEL (WUS) and the CLAVATA1, 2 and 3 (CLV) genes that are involved in size regulation of the meristem. In a zll loss-of-function background wus has a negative effect whereas clv mutations have a positive effect on meristem size. We propose that ZLL buffers meristem stability non-cell-autonomously by ensuring the critical number of apical cells required for proper meristem function.

Arabidopsis thaliana is one of the most studied plant model systems. Completing the genomic sequence of A. thaliana has provided new opportunities for physiological and biochemical studies. While its small size is advantageous for genetic studies, the plant's low biomass makes it difficult to obtain enough plant material for biochemical and physiological research. The small size and rosette leaf structure, combined with the sensitivity of the apical meristem to flooding, make hydroponic growth of this model plant difficult. A few systems for hydroponic culture of Arabidopsis have been described. Gibeaut et al. (1997) introduced the use of rockwool for Arabidopsis hydroponic culture. We have improved this system by introducing small-volume plastic containers with improved plugs to support the rockwool. This method is simpler than the original setup and provides improved germination and growth. The smaller containers enable the use of this system in growth chambers or small growth rooms for a large number of parallel experiments.

In genetic hybrids, nucleolus formation on chromosomes inherited from only one parent is the epigenetic phenomenon, nucleolar dominance. By using Arabidopsis suecica, the allotetraploid hybrid of Arabidopsis thaliana and Arabidopsis arenosa, natural variation in nucleolar dominance was found to occur, providing a unique opportunity to examine homologous nucleolus organizer regions (NORs) in their active and inactive states. In A. suecica strain LC1, NORs derived from A. arenosa are active, whereas A. thalianaderived NORs are silenced. In A. suecica strain 9502, NORs of both parental species are active. When active, NORs are partially, but not fully, decondensed. Both active and inactive LC1 NORs colocalize with the nucleolus, contradicting the long-standing assumption that rRNA gene transcription drives nucleolus association. Collectively, these observations clarify the relationships among NOR chromatin topology, rRNA gene transcription, and NOR–nucleolus associations. A. suecica strains LC1 and 9502 have each lost one pair of A. thaliana NORs during evolution, and amplified fragmentlength polymorphism analysis further indicates that these strains are genetically very similar. These data suggest that nucleolar dominance can result from subtle genetic or epigenetic variation but is not a trait fundamental to a given interspecies hybrid combination