Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays

Cytosolic aldolase is a ripening related enzyme in strawberry fruits (Fragaria x ananassa)

Two aldolase isoenzymes have been isolated from ripe strawberry fruits (Fragaria x ananassa cv. Camarosa and Elsanta) and partially purified by DEAE anion exchange and Sephacryl size exclusion chromatography. The isoenzymes were identified as class I cytosol and plastid aldolase on the basis of their chromatographic behavior on DEAE-cellulose columns, native molecular weight, pH optimum pattern, Km value for D-fructose-1,6-bisphosphate, tendency to be inactivated by lower pH values and SDS-PAGE subunit determination of 40 and 38 kDa, respectively. Total aldolase activity and distribution of both aldolase isoenzymes was also investigated at different stages of strawberry fruit ripening. Strawberries in the green and white ripening stage showed the same ratio of the two isoenzymes as green leaves with 15 and 8% cytosol aldolase activity, respectively. During strawberry fruit development the overall total aldolase activity decreased until the pink ripening stage and then increased due to a rise of cytosol aldolase yielding up to 75% in red strawberries. A cDNA putatively encoding the cytosolic form of aldolase in strawberry was cloned during the course of this study. Both microarray and RNA gel blot analyses showed that the cytosolic aldolase gene expression is induced during ripening as detected for the cytosolic aldolase enzyme. We suggest that induction of the cytosolic aldolase both at the levels of transcription and translation might be part of a ripening related stress response in the receptacle tissue.

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.

Acetyl-coa: alcohol acetyltransferase activity and aroma formation in ripening melon fruits

Melon varieties (Cucumis melo L.) differ in a range of physical and chemical attributes. Sweetness and aroma are two of the most important factors in fruit quality and consumer preference. Volatile acetates are major components of the headspace of ripening cv. Arava fruits, a commercially important climacteric melon. In contrast, volatile aldehydes and alcohols are most abundant in cv. Rochet fruits, a nonclimacteric melon. The formation of volatile acetates is catalyzed by alcohol acetyltransferases (AAT), which utilize acetyl-CoA to acetylate several alcohols. Cell-free extract derived from Arava ripe melons exhibited substantial levels of AAT activity with a variety of alcohol substrates, whereas similar extracts derived from Rochet ripe melons had negligible activity. The levels of AAT activity in unripe Arava melons were also low but steadily increased during ripening. In contrast, similar extracts from Rochet fruits displayed low AAT activity during all stages of maturation. In addition, the benzyl- and 2-phenylethyl-dependent AAT activity levels seem well correlated with the total soluble solid content in Arava fruits.

Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray

Full-length cDNAs are essential for functional analysis of plant genes. Using the biotinylated CAP trapper method, we constructed full-length Arabidopsis cDNA libraries from plants in different conditions, such as drought-treated, cold-treated, or unstressed plants, and at various developmental stages from germination to mature seed. We prepared a cDNA microarray using approximately 1300 full-length Arabidopsis cDNAs to identify drought- and cold-inducible genes and target genes of DREB1A/CBF3, a transcription factor that controls stress-inducible gene expression. In total, 44 and 19 cDNAs for drought- and cold-inducible genes, respectively, were isolated, 30 and 10 of which were novel stress-inducible genes that have not been reported as drought- or cold-inducible genes previously. Twelve stress-inducible genes were identified as target stress-inducible genes of DREB1A, and six of them were novel. On the basis of RNA gel blot and microarray analyses, the six genes were identified as novel drought- and cold-inducible genes that are controlled by DREB1A. Eleven DREB1A target genes whose genomic sequences have been registered in the GenBank database contained the dehydration-responsive element (DRE) or DRE-related CCGAC core motif in their promoter regions. These results show that our full-length cDNA microarray is a useful material with which to analyze the expression pattern of Arabidopsis genes under drought and cold stresses, to identify target genes of stress-related transcription factors, and to identify potential cis-acting DNA elements by combining the expression data with the genomic sequence data.

Phytochrome regulation of nuclear gene expression in plants

The photoregulation of gene expression in higher plants was extensively studied during the 1980s, in particular the light-responsive cis -acting elements and trans -acting factors of the Lhcb and rbcS genes. However, little has been discovered about: (1) which plant genes are regulated by light, and (2) which photoreceptors control the expression of these genes. In the 1990s, the functional analysis of the various photoreceptors has progressed rapidly using photoreceptor-deficient mutants, including those of the phytochrome gene family. More recently however, advanced techniques for gene expression analysis, such as fluorescent differential display and DNA microarray technology, have become available enabling the global identification of genes that are regulated by particular photoreceptors. In this paper we describe distinct and overlapping effects of individual phytochromes on gene expression in Arabidopsis thaliana.

A genomic perspective on plant transcription factors

Data from the Arabidopsis genome project suggest that more than 5% of the genes of this plant encode transcription factors. The necessity for the use of genomic analytical approaches becomes clear when it is considered that less than 10% of these factors have been genetically characterized. A variety of tools for functional genomic analyses in plants have been developed over the past few years. The availability of the full complement of Arabidopsis transcription factors, together with the results of recent studies that illustrate some of the challenges to their functional characterization, now provides the basic framework for future analyses of transcriptional regulation in plants.