Biological rhythms are ubiquitous in eukaryotes, and the best understood of these occur with a period of approximately a day – circadian rhythms. Such rhythms persist even when the organism is placed under constant conditions, with a period that is close, but not exactly equal, to 24 h, and are driven by an endogenous timer – one of the many ‘biological clocks’. In plants, research into circadian rhythms has been driven forward by genetic experiments using Arabidopsis. Higher plant genomes include a particularly large number of genes involved in metabolism, and circadian rhythms may well provide the necessary coordination for the control of these – for example, around the diurnal rhythm of photosynthesis – to suit changing developmental or environmental conditions. The endogenous timer must be flexible enough to support these requirements. Current research supports this notion most strongly for the input pathway, in which multiple photoreceptors have been shown to mediate light input to the clock. Both input and output components are now related to putative circadian oscillator mechanisms by sequence homology or by experimental observation. It appears that the pathways linking some domains of the basic clock model may be very short indeed, or the mechanisms of these domains may overlap. Components of the first plant circadian output pathway to be identified unequivocally will help to determine exactly how many output pathways control the various phases of overt rhythms in plants. contents Summary 175 I. the circadian system 176 II. overt circadian rhythms 177 III. photoperiodism 183 IV. oscillator theory and practice 186 V. phototransduction pathways 190 VI. conclusions 192 Acknowledgements 193 References 193

Axi 1 is an auxin independent gene which is characterized only in Nicotiana tabacum and Arabidopsis thaliana. This gene confers on protoplasts the ability to grow in culture not only in the absence of auxin but also at high levels of auxin concentrations. In this study, axi 1 gene was isolated from Pisum sativum and nucleotide sequences of this gene was searched. The nucleotide sequences from Pisum sativum axi 1 gene were compared with the nucleotide sequences of Arabidopsis thaliana axi 1 gene and based on this data, 71.918 % homology between nucleotide sequences and 80.588 % homology between peptide sequences were found. The nucleotide sequences from Pisum sativum axi 1 gene were also compared with the nucleotide sequences of Arabidopsis thaliana axi 1 gene, and as a result, 82.111% homology between nucleotide sequences and also peptide sequences were determined

We report here on the identification in Arabidopsis thaliana of a new family of transposable elements named Hairpin. These elements are related to foldback transposons (FTs), a large and heterogeneous group of transposable elements first described in Drosophila and recently in Solanaceae. Hairpin elements are the first family of FTs reported in Arabidopsis thaliana and the first family of FTs of type 3 to be described in the plant kingdom. In contrast to previous FTs described, Hairpin appears to be a homogeneous family in size (238 +/- 7 bp) as well as in structure. Hairpin elements are dispersed in the Arabidopsis genome and Southern hybridization revealed that they are present in relatively low copy numbers. Finally, we discuss the potential usefulness of these elements in studying the phylogenetic relationship between Arabidopsis ecotypes.

The frequency and selective impact of deleterious mutations are fundamental parameters in evolutionary theory, yet they have not been directly measured in a plant species. To estimate these quantities, we allowed spontaneous mutations to accumulate for 10 generations in 1,000 inbred lines of the annual, self-fertilizing plant Arabidopsis thaliana and assayed fitness differences between generations 0 and 10 in a common garden. Germination rate, fruit set, and number of seeds per fruit each declined by less than 1% per generation in the mutation lines, and total fitness declined by 0.9% per generation. Among-line variances increased in the mutation lines for all traits. Application of an equal-effects model suggests a downwardly biased genomic deleterious mutation rate of 0.1 and a upwardly biased effect of individual mutations on total fitness of 20%. This genomic deleterious mutation rate is consistent with estimates of nucleotide substitution rates in flowering plants, the genome size of Arabidopsis, and the equilibrium inbreeding depression observed in this highly selfing plant species.

A modified protocol for differential display of mRNA was used to identify and clone genes expressed in developing Arabidopsis thaliana seeds. Two novel embryo-specific genes designated ATS1 and ATS3 (Arabidopsis thaliana seed gene) were identified. In suit hybridization showed that, spatially, ATS1 is expressed in a pattern similar to the Arabidopsis GEAl gene and that ATS3 is expressed in a pattern similar to the Arabidopsis seed storage protein genes. Southern analysis of Arabidopsis genomic DNA indicated that ATS1 is a member of a small gene family and that ATS3 is present as a single copy in the diploid genome. Sequence analysis of both genes showed that ATS1 is similar to the rice EFA27 gene and that ATS3 is unique. Western analysis and light level immunocytochemistry using antisera raised against the putative ATS1 and ATS3 translation products verified that ATS1 and ATS3 proteins are seed-specific and accumulate in a spatial pattern similar to their respective transcripts. Taken together, these data show that ATS1 and ATS3 are novel embryo-specific genes in Arabidopsis.

Methylation of plant DNA occurs at in any sequence context, and as the Arabidopsis methyltransferase, METI, preferentially methylates cytosines in CG dinucleotides, it is likely that Arabidopsis has other methyltransferases with different target specificities. We have identified five additional genes encoding putative DNA methyltransferases. Three of these genes are very similar to METI throughout the coding region; these genes probably arose by a series of gene duplication events, the most recent giving rise to METIIa and METIIb, METIIa and b are expressed at low levels in vegetative and floral organs and the level of transcripts is not affected by the introduction of a METI antisense transgene, nor do the METII enzymes substitute for the reduced activity of METI in methylating CG dinucleotides. METIII is not essential as it encodes a truncated protein. Two other genes encode a second class of DNA methyltransferase with the conserved motifs characteristic of cytosine methyltransferases, but with little homology to the METI-like methyltransferases through the remainder of the protein. These two methyltransferases are characterized by the presence of a chromodomain inserted within the methyltransferase domain, suggesting that they may be associated with heterochromatin. Both these genes are transcribed at low levels in vegetative and reproductive tissues.

We have previously isolated two closely related genes (ATCYP1 and ATCYP2) each encoding a cytosolic cyclophilin of Arabidopsis thaliana. Here we tested expression patterns of these two genes by Northern analysis and by histochemical analysis with transgenic punts carrying the promoter: beta-glucuronidase (GUS) fusion. The results showed that ATCYP1 is predominantly transcribed in vascular tissue and flowers, but ATCYP2 is at higher levels in younger leaves. The different expression patterns seemed to be conferred by the quite different promoter structures carrying various cis elements. Our finding suggests that the two cyclophilin have different roles in Arabidopsis thaliana cells

Using subtractive hybridization, we have isolated a cDNA clone representing a blue light-regulated gene in Arabidopsis thaliana. The clone encodes for the auxin-binding glutathione S-transferae Atpm24.1 (GST; EC2.5.1.18). In Arabidopsis thaliana seedlings, transcript levels of this GST are severely diminished in the phototropism null mutant, JK218. In seedlings of the wild-type parent, transcript levels increase with fluence of blue-light irradiation. The fluences of blue light that up-regulate this GST correspond to the fluences that induce first positive phototropism in Arabidopsis. The blue light up-regulation of Atpm24.1 transcription is evident within 20 min. of irradiation. This time corresponds well to the kinetics with which phototropic curvature develops. Atpm24.1 is regulated by blue light but not by red light. Based on these data, a role for this GST in phototropism is suggested.

Elicitation of Arabidopsis thaliana (L.) Heynh. suspension cultures with the bacterial protein harpin (from Pseudomonas syringae pv. syringae) induced the activation of two kinases of 39 and 44 kDa, as demonstrated by in-gel kinase assays using myelin basic protein (MBP) as a substrate. Both these kinases appeared to be tyrosine-phosphorylated upon activation, as demonstrated by treatment with tyrosine phosphatase and immunoprecipitation using an anti-phosphotyrosine monoclonal antibody. An inhibitor of mammalian mitogen-activated protein kinase (MAPK) activation, PD98059, inhibited harpin-induced MBPK activation, but did not inhibit the activity of these kinases. PD98059 also inhibited harpin-induced programmed cell death and defence gene expression, suggesting the involvement of harpin-induced MAPKs in defence responses in Arabidopsis thaliana.