Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs

Nearly 7000 Arabidopsis thaliana -expressed sequence tags (ESTs) from 10 cDNA libraries have been sequenced, of which almost 5000 non-redundant tags have been submitted to the EMBL data bank. The quality of the cDNA libraries used is analysed. Similarity searches in international protein data banks have allowed the detection of significant similarities to a wide range of proteins from many organisms. Alignment with ESTs from the rice systematic sequencing project has allowed the detection of amino acid motifs which are conserved between the two organisms, thus identifying tags to genes encoding highly conserved proteins. These genes are candidates for a common framework in genome mapping projects in different plants.     

Photomodulation of growth and specific changes in fatty acid amounts in internodes of green Vigna sinensis L.

First internode growth of green Vigna sinensis L. can be widely modified by light or dark treatments. In all the treatments used there is a good correlation between the internode growth and the rate of C_18-1 accumulation. None of the other fatty acids show such a correlation.Abbreviations C_16-0 palmitoic acid - C₁₇ heptadecanoic acid - C_18-0 stearic acid - C_18-1 octadecenoic acid - C_18-2 linoleic acid - C_18-3 linolenic acid - D darkness - DW dry weight - FR far-red light - FW fresh weight - P_FR phytochrome in the FR absorbing form - R red light - W white light     

Oleic acid metabolism: A biochemical marker for studying photoregulation of epicotyl elongation in Vigna unguiculata

Oleic acid metabolism can be considered to be an indicator of growth photoregulation in cowpea ( Vigna unguiculata Westphal cv. M53) epicotyls. Phosphatidylcholine and phosphatidylethanolamine are the two lipid classes concerned in the photoregulation of oleic acid accumulation. The incorporation of radioactive precursors in internodes of whole plants has shown that there is de novo synthesis of these phospholipids during the light dependent growth process.
The variations in oleic acid content were used to study the photocontrol of elongation in segments excised from the apical part of the epicotyl. In this system, as in whole plants, oleic acid was the only fatty acid showing significant variation related to the light/dark treatments. Differences in photoresponse between excised intenode segments and internodes in whole plants are discussed.     

FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants

A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented database, FLAGdb/FST (http://genoplante-info.infobiogen.fr). The main scope of FLAGdb/FST is to help biologists to find the FSTs that interrupt the genes in which they are interested. FSTs are anchored to the genome sequences of A.thaliana and positions of both predicted genes and FSTs are shown graphically on sequences. Requests to locate the genomic position of a query sequence are made using BLAST programs. The response delivered by FLAGdb/FST is a graphical representation of the putative FSTs and of predicted genes in a 20 kb region.     

Stem Extension Rate in Light-Grown Plants : Effects of Photo- and Thermoperiodic Treatments on the Endogenous Circadian Rhythm in Chenopodium rubrum

Low temperature pulses have two effects on the circadian rhythm exhibited by stem extension rate of green Chenopodium rubrum plants. First, low temperature pulses have the same effect on the phasing of the rhythm as a dark period interrupting continuous light. Second, low temperature pulses stimulate stem extension rate during the 10 hours immediately following the end of the pulse. A difference in temperature between soil and air increases this effect. In any case, it is the change in temperature which is essential and not a specific temperature. Effects of light and temperature on phasing and amplitude of the rhythm explain why the maximal stem growth is observed under normal photo-thermoperiodic conditions, i.e. a high temperature during the photoperiod and a low temperature during the dark period.     

Genetic Variability in Carbon Fixation, Sucrose-P-Synthase and ADP Glucose Pyrophosphorylase in Maize Plants of Differing Growth Rate

The net photosynthetic rate and the activities of ribulose 1,5 bisphosphate carboxylase (RubisCo), phosphoenolpyruvate carboxylase, sucrose-P-synthase, and ADP glucose-pyrophosphorylase, key enzymes of the leaf carbohydrate metabolism were compared in eight maize (Zea mays L.) genotypes presenting large differences in growth rate. The sucrose-P-synthase activity varied in the ratio 1 to 3 from the less active to the more active genotype and this variation was highly correlated with those in growth rate. ADP glucose pyrophosphorylase activity was not significantly different from one genotype to another whatever the basis for expression, leaf area, or soluble protein. The photosynthetic rate varied with similar amplitude (1:1) to the RubisCo activity or RubisCo quantity but the correlation with growth rate was highly significant for photosynthesis and nonsignificant for RubisCo or phosphoenolpyruvate carboxylase. So, in our series of genotypes the sucrose synthesis capacities as expressed by sucrose phosphate synthase activity seem to have a good predicting value for mean growth rate at a young stage.     

Stem extension rate in light-grown plants. Evidence for an endogenous circadian rhythm in Chenopodium rubrum

Stem extension in light-grown plants of Chenopodium rubrum L. ecotype selection 184 (50°10'N; 150°35'W) was recorded continuously for periods up to one week at constant temperature. Stem extension rate measurements were made with linear voltage-displacement transducer devices. At the beginning of experiments, the 3rd intenode above the cotyledons was about 5 mm long. Stem extension rate exhibited a rhythmic behaviour in continuous white light (20 W m⁻²), and in continuous darkness with a period of approximately 23 h. In continuous darkness, the amplitude of the rhythm damped out very quickly after 24 h and a second peak was just measurable. The mean value of the stem extension rate was dependent on the light fluence before the experiments. This overt rhythm, which could be observed at the individual plant or even internode level, exhibited the characteristics of an endogenous circadian rhythm. There was no correlation of the peak time to local time. The peak time was determined by the time of transfer from dark to light for dark periods equal to or longer than 8 h, and the phase was shifted by the time of transfer from light to dark at the proper phase of a pre-existing rhythm.     

The arabinose kinase,ARA1, gene of Arabidopsis is a novel member of the galactose kinase gene family

The arabinose-sensitive ara1-1 mutant of Arabidopsis is deficient in arabinose kinase activity. A candidate for the ARA1 gene, ISA1, has been previously identified through the Arabidopsis genome sequencing initiative. Here we demonstrate that (1) the ARA1 gene coincides with ISA1 in a positional cloning strategy; (2) there are mutations in the ISA1 gene in both the ara1-1 mutant and an intragenic suppressor mutant; and (3) the ara1-1 and suppressor mutant phenotypes can be complemented by the expression of the ISA1 cDNA in transgenic plants. Together these observations confirm that ISA1 is the ARA1 gene. ARA1 is a member of the galactose kinase family of genes and represents a new substrate specificity among this and other families of sugar kinases. A second gene with similarities to members of the galactose kinase gene family has been identified in the EST database. A 1.8 kb cDNA contained an open reading-frame predicted to encode a 496 amino acid polypeptide. The GAL1 cDNA was expressed in a galK mutant of Escherichia coli and in vitro assays of extracts of the strain expressing GAL1 confirmed that the cDNA encodes a galactose kinase activity. Both GAL1 and ARA1 cross-hybridise at low stringency to other sequences suggesting the presence of additional members of the galactose kinase gene family.     

Ultrastructural detection of sucrose synthase distribution in developing maize leaves

Summary A developing maize leaf grows by the activity of a basal meristematic region and an adjacent elongating zone, resulting in a morphological and functional gradient along the leaf. We have used this system to detect the spatial and temporal expression of an enzyme, sucrose synthase, which plays a pivotal role in the sucrose import-export transition which occurs along a monocotyledon leaf. Immunogold labeling was used to detect the cellular and sub-cellular distribution of sucrose synthase (SS) at the electron microscopical level; the protein was visualized using a polyclonal antiserum on embedded tissue sections. Immunolabel was observed in the cytosol of dividing meristematic cells, expanding cells of the elongation zone, and in differentiating cells of young photosynthetic tissue. In fully differentiated leaf tissue, however, the protein was no longer immuno-detectable in photosynthetic cells, but was present in the guard and subsidiary cells of stomata and in companion cells within the phloem tissue of vascular bundles. The tissue- and cell-specific localization of sucrose synthase changes along the growing leaf as a function of the developmental state and the associated need for sucrose import or export.     

Formation of the Arabidopsis pentatricopeptide repeat family

In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.