Dimitra Milioni

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana

The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

GENOMIC ORGANIZATION OF HSP90 GENE FAMILY IN ARABIDOPSIS

We have isolated six members of the hsp90 gene family from Arabidopsis thaliana. Three genes designated hsp81.2, 81.3 and 81.4 are clustered within a 15 kb genomic region while two of these are 1.5 kb apart in a head-to-head orientation. The deduced amino acid sequence shows that the members can be divided into two types. The hsp81.1, 81.2, 81.3 and 81.4 genes comprise the cytosolic hsp90 type having few introns. However, the hsp88.1 and 89.1 genes comprising the organelle type are composed of 18 or 19 introns. Sequence comparison showed there is high homology among the cytosolic members while there is less homology among the organelle members. The expression of the hsp90 genes and mRNA accumulation in plants and calli is very low at control temperatures and is strongly induced by heat-shock. Arsenite stress strongly stimulates the expression of this gene family.

Combinatorial interaction of cis elements specifies the expression of the Arabidopsis AtHsp90-1 gene.

The promoter region of the ArabidopsisAtHsp90-1 gene is congested with heat shock elements and stress response elements, as well as with other potential transcriptional binding sites (activating protein 1, CCAAT/enhancer-binding protein element, and metal regulatory element). To determine how the expression of this bona fideAtHsp90-1 gene is regulated, a comprehensive quantitative and qualitative promoter deletion analysis was conducted under various environmental conditions and during development. The promoter induces gene expression at high levels after heat shock and arsenite treatment. However, our results show that the two stress responses may involve common but not necessarily the same regulatory elements. Whereas for heat induction, heat shock elements and stress response elements act cooperatively to promote high levels of gene expression, arsenite induction seems to require the involvement of activating protein 1 regulatory sequences. In stressed transgenic plants harboring the full-length promoter, β-glucuronidase activity was prominent in all tissues. Nevertheless, progressive deletion of the promoter decreases the level of expression under heat shock and restricts it predominantly in the two meristems of the plant. In contrast, under arsenite induction, proximal sequences induceAtHsp90-1 gene expression only in the shoot meristem. Distally located elements negatively regulate AtHsp90-1gene expression under unstressed conditions, whereas flower-specific regulated expression in mature pollen grains suggests the prominent role of the AtHsp90-1 in pollen development. The results show that the regulation of developmental expression, suppression, or stress induction is mainly due to combinatorial contribution of the cis elements in the promoter region of the AtHsp90-1gene.

Approaches to understanding the functional architecture of the plant cell wall.

Cell wall polysaccharides are some of the most complex biopolymers known, and yet their functions remain largely mysterious. Advances in imaging methods permit direct visualisation of the molecular architecture of cell walls and the modifications that occur to polymers during growth and development. To address the structural and functional relationships of individual cell wall components, we need to better characterise a broad range of structural and architectural alterations in cell walls, appearing as a consequence of developmental regulation, environmental adaptation or genetic modification. We have developed a rapid method to screen large numbers of plants for a broad range of cell wall phenotypes using Fourier transform infrared microspectroscopy and Principal Component Analysis. We are using model systems to uncover the genes that encode some of the cell-wall-related biosynthetic and hydrolytic enzymes, and structural proteins.

Breeding, molecular markers and molecular biology of the olive tree

Olive (Olea europaea L.) is a typical crop species of the Mediterranean Basin. A number of cultivars were selected and propagated mainly vegetatively over the centuries for their qualitative and quantitative traits. Due to the long juvenile phase of the tree, few breeding programs have been performed. Therefore the most appropriate process is a selection scheme from heterogeneous populations or cultivars varying in oil quantity and quality, harvest regimes, and biotic and abiotic resistance. Molecular marker techniques have been applied recently on olive to relate, identify, distinguish and characterize different cultivars or genotypes and in order to provide information on olive origin and dispersal and to evaluate olive germplasm for traits with agronomical importance. To understand the regulation of biosynthetic pathways of oil and antioxidants on the molecular level, we have isolated a number of genes encoding for key enzymes in fatty acid and antioxidant biosynthesis, modification and triacylglycerol storage. The gene expression during fruit growth and seed development as well as their transient and temporal expression in different tissues is discussed in relation to storage of fatty acids and to provision of signaling molecules important in plant defense mechanisms and reproduction.

The thanatos mutation in Arabidopsis thaliana cellulose synthase 3 (AtCesA3) has a dominant‐negative effect on cellulose synthesis and plant growth

Genetic functional analyses of mutants in plant genes encoding cellulose synthases (CesAs) have suggested that cellulose deposition requires the activity of multiple CesA proteins. Here, a genetic screen has led to the identification of thanatos (than), a semi-dominant mutant of Arabidopsis thaliana with impaired growth of seedlings. Homozygous seedlings of than germinate and grow but do not survive. In contrast to other CesA mutants, heterozygous plants are dwarfed and display a radially swollen root phenotype. Cellulose content is reduced by approximately one-fifth in heterozygous and by two-fifths in homozygous plants, showing gene-dosage dependence. Map-based cloning revealed an amino acid substitution (P578S) in the catalytic domain of the AtCesA3 gene, indicating a critical role for this residue in the structure and function of the cellulose synthase complex. Ab initio analysis of the AtCesA3 subdomain flanking the conserved proline residue predicted that the amino acid substitution to serine alters protein secondary structure in the catalytic domain. Gene dosage-dependent expression of the AtCesA3 mutant gene in wild-type A. thaliana plants resulted in a than dominant-negative phenotype. We propose that the incorporation of a mis-folded CesA3 subunit into the cellulose synthase complex may stall or prevent the formation of functional rosette complexes.

Brassinosteroid nuclear signaling recruits HSP90 activity

Heat shock protein 90 (HSP90) controls a number of developmental circuits, and serves a sophisticated and highly regulatory function in signaling pathways. Brassinosteroids (BRs) control many aspects of plant development. Genetic, physiological, cytological, gene expression, live cell imaging, and pharmacological approaches provide conclusive evidence for HSP90 involvement in Arabidopsis thalianaBR signaling. Nuclear-localized HSP90s translocate to cytoplasm when their activity is blocked by the HSP90 inhibitor geldanamycin (GDA). GDA treatment promoted the export of BIN2, a regulator of BR signaling, from the nucleus into the cytoplasm, indicating that active HSP90 is required to sustain BIN2 in the nucleus. HSP90 nuclear localization was inhibited by brassinolide (BL). HSP90s interact with BIN2 in the nucleus of untreated cells and in the cytoplasm of BL-treated cells, showing that the site-specific action of HSP90 on BIN2 is controlled by BRs. GDA and BL treatments change the expression of a common set of previously identified BR-responsive genes. This highlights the effect of active HSP90s on the regulation of BR-responsive genes. Our observations reveal that HSP90s have a central role in sustaining BIN2 nuclear function. We propose that BR signaling is mediated by HSP90 activity and via trafficking of BIN2-HSP90 complexes into the cytoplasm.

A RING Domain Gene Is Expressed in Different Cell Types of Leaf Trace, Stem, and Juvenile Bundles in the Stem Vascular System of Zinnia

The in vitro zinnia (Zinnia elegans) mesophyll cell system, in which leaf mesophyll cells are induced to transdifferentiate into tracheary elements with high synchrony, has become an established model for studying xylogenesis. The architecture of the stem vascular system of zinnia cv Envy contains three anatomically distinct vascular bundles at different stages of development. Juvenile vascular strands of the subapical region develop into mature vascular strands with leaf trace segments and stem segments. Characteristic patterns of gene expression in juvenile, leaf trace, and stem bundles are revealed by a molecular marker, a RING domain-encoding gene, ZeRH2.1, originally isolated from a zinnia cDNA library derived from differentiating in vitro cultures. Using RNA in situ hybridization, we show that ZeRH2.1 is expressed preferentially in two specific cell types in mature zinnia stems. In leaf trace bundles, ZeRH2.1 transcript is abundant in xylem parenchyma cells, while in stem bundles it is abundant in phloem companion cells. Both of these cell types show wall ingrowths characteristic of transfer cells. In addition, ZeRH2.1 transcript is abundant in some phloem cells of juvenile bundles and in leaf palisade parenchyma. The complex and developmentally regulated expression pattern of ZeRH2.1 reveals heterogeneity in the vascular anatomy of the zinnia stem. We discuss a potential function for this gene in intercellular transport processes.

Gene expression during heat-shock in embryogenic carrot cell lines

We have isolated an hsp90 gene from carrot (Daucus carota). The deduced amino acid sequence from this cDNA revealed its similarity to the organelle-type HSP90 protein. It has high homology to other plant organelle-isoforms and shows similar homology to both cytoplasmic and prokaryotic HSP90s. To study the regulation of gene expression during heat-shock, two embryo-specific DC8 and DC59 genes, a tubulin gene and an hsp90 gene were monitored in two embryogenic heat-stressed carrot cell lines. The expression of DC8, a LEA and DC59, an oleosin gene, decreased in both cell lines. In addition, there was a progressive degradation of the accumulated messages with time. The expression of hsp90 gene was induced in both cell lines but with a different pattern of transcript accumulation. These results indicate that the haploid cell line responds differently from the diploid cell line and there is differential transcriptional activity in both cell lines during heat-stress.

Biotechnology Towards Energy Crops

New crops are gradually establishing along with cultivation systems to reduce reliance on depleting fossil fuel reserves and sustain better adaptation to climate change. These biological assets could be efficiently exploited as bioenergy feedstocks. Bioenergy crops are versatile renewable sources with the potential to alternatively contribute on a daily basis towards the coverage of modern society’s energy demands. Biotechnology may facilitate the breeding of elite energy crop genotypes, better suited for bio-processing and subsequent use that will improve efficiency, further reduce costs, and enhance the environmental benefits of biofuels. Innovative molecular techniques may improve a broad range of important features including biomass yield, product quality and resistance to biotic factors like pests or microbial diseases or environmental cues such as drought, salinity, freezing injury or heat shock. The current review intends to assess the capacity of biotechnological applications to develop a beneficial bioenergy pipeline extending from feedstock development to sustainable biofuel production and provide examples of the current state of the art on future energy crops.