Identification of the SAAT Gene Involved in Strawberry Flavor Biogenesis by Use of DNA Microarrays

Aharoni, Asaph; Keizer, L.C.P.; Bouwmeester, Harro J.; Sun, Zhian; Alvarez-Huerta, Mayte; Verhoeven, H. A.; Blaas, J.; Houwelingen, Adele M. M. L. van; Vos, Ric C. H. de; Voet, Hilko van der; Jansen, Ritsert C.; Guis, Monique; Mol, J.G.J.; Davis, Ronald W.; Schena, Mark; Tunen, Arjen J. van; O’Connell, Ann P.

doi:10.2307/3870992

Cited by 84 publications

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“…The first study identified strawberry alcohol acetyl transferase as a critical enzyme in the production of volatiles esters. The associated transcript increased during fruit ripening and the recombinant protein catalyzes the appropriate syntheses from a variety of substrates in E. coli [23]. A recent functional-genomics study characterized Nerolidol Synthase 1 , the enzyme that catalyzes the formation of the flavor compounds linalool and nerolidol from geranyl diphosphase and farnesyl diphosphate, respectively.…”

Section: Discussionmentioning

confidence: 99%

Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)

et al. 2005

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Background: Cultivated strawberry (Fragaria × ananassa) represents one of the most valued fruit crops in the United States. Despite its economic importance, the octoploid genome presents a formidable barrier to efficient study of genome structure and molecular mechanisms that underlie agriculturally-relevant traits. Many potentially fruitful research avenues, especially large-scale gene expression surveys and development of molecular genetic markers have been limited by a lack of sequence information in public databases. As a first step to remedy this discrepancy a cDNA library has been developed from salicylate-treated, whole-plant tissues and over 1800 expressed sequence tags (EST's) have been sequenced and analyzed.

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Section: Discussionmentioning

confidence: 99%

Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)

et al. 2005

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“…Recently, we have shown that the regeneration can also be used in the preparation of single-stranded DNA using an alkali elution to separate the two strands, followed by the nonionic elution of the biotinylated single strand to regenerate the beads (Holmberg, unpublished). The single-stranded template can subsequently be used for various applications, including in vitro mutagenesis [32], pyrosequencing [33], or transcript profiling [34][35][36].…”

Section: Discussionmentioning

confidence: 99%

The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures

et al. 2005

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The biotin-streptavidin interaction can be reversibly broken using water at elevated temperaturesThe biotin-streptavidin system is the strongest noncovalent biological interaction known, having a dissociation constant, K d , in the order of 4610 214 M. The strength and specificity of the interaction has led it to be one of the most widely used affinity pairs in molecular, immunological, and cellular assays. However, it has previously been impossible to re-use any streptavidin solid support, since the conditions needed to break the interaction with biotin has led to the denaturation of the streptavidin. Here, we show that a short incubation in nonionic aqueous solutions at temperatures above 707C can efficiently break the interaction without denaturing the streptavidin tetramer. Both biotin and the streptavidin remain active after dissociation and both molecules can therefore be re-used. The efficiency of the regeneration allowed solid supports with streptavidin to be used many times, here exemplified with the multiple re-use of streptavidin beads used for sample preparation prior to automated DNA sequencing. The results suggest that streptavidin regeneration can be introduced as an improvement in existing methods and assays based on the streptavidin system as well as emerging solid phase applications in fields, such as microfluidics and nanotechnology. IntroductionThe strong interaction between avidin and biotin was discovered as early as 1941 [1]. Avidin is a protein commonly purified from chicken egg white while biotin is a vitamin found in all cells. Streptavidin, a bacterial homologous protein to avidin, isolated from the actinobacterium Streptomyces avidinii, is more frequently used than avidin and is commercially available also in a number of engineered forms. The structure of the biotin-streptavidin complex has been described by several groups [2,3], showing a b-barrel structure of streptavidin binding biotin into its interior. The binding between avidin/streptavidin and biotin has long been regarded as the strongest, noncovalent, biological interaction known, having a dissociation constant, K d , in the order of 4610 214 M [4]. The bond forms very rapidly and is stable in wide ranges of pH and temperature [1,5].The strong interaction has led to a large number of research and diagnostic applications using avidin-biotin or streptavidin-biotin technology. The strength and reliability of the interaction underlie its importance in biotechnology, but the interaction is also a model for high-affinity receptor ligand binding. In most assays, streptavidin is coupled to a solid phase, such as a magnetic bead, a microtiter plate, or a biosensor chip, while biotin is coupled to the moiety of interest, often a nucleic acid, protein, or antibody. However, harsh conditions, such as formamide treatment combined with high temperatures, have been required to separate biotin from streptavidin, resulting in not only denatured streptavidin molecules [5] but also in limitations of downstream applications due to deterioration ...

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“…T ranscript profiling has the potential to reveal transcriptional hierarchy during development for thousands of genes, as well as providing expression data for many genes of unknown function (1,2). This is especially true when expression patterns can be obtained for well defined tissues at specific developmental stages.…”

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confidence: 99%

A transcriptional roadmap to wood formation

Hertzberg

Aspeborg

Schrader

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

440

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The large vascular meristem of poplar trees with its highly organized secondary xylem enables the boundaries between different developmental zones to be easily distinguished. This property of wood-forming tissues allowed us to determine a unique tissuespecific transcript profile for a well defined developmental gradient. RNA was prepared from different developmental stages of xylogenesis for DNA microarray analysis by using a hybrid aspen unigene set consisting of 2,995 expressed sequence tags. The analysis revealed that the genes encoding lignin and cellulose biosynthetic enzymes, as well as a number of transcription factors and other potential regulators of xylogenesis, are under strict developmental stage-specific transcriptional regulation.T ranscript profiling has the potential to reveal transcriptional hierarchy during development for thousands of genes, as well as providing expression data for many genes of unknown function (1, 2). This is especially true when expression patterns can be obtained for well defined tissues at specific developmental stages. However, this is technically demanding and so far there are no reports demonstrating tissue-specific analysis on cell types from a single developmental sequence. We have studied the developing secondary xylem of poplar, which is highly organized with easily recognized and distinct boundaries between the different developmental stages. Wood formation is initiated in the vascular cambium. Cambial derivatives develop into xylem cells through the processes of division, expansion, secondary wall formation, lignification, and finally, programmed cell death. The large physical size of the vascular meristem in trees offers a unique possibility to obtain samples from defined developmental stages by tangential cryo sectioning (3). To determine the steady-state mRNA levels at specific stages during the ontogeny of wood formation in Populus tremula ϫ Populus tremuloides (hybrid aspen) we sampled 30-m-thick sections through the wood development region and subsequently analyzed the samples by using a spotted cDNA-microarray (4) consisting of 2,995 unique ESTs from hybrid aspen. Our study provides a unique global examination of gene expression patterns that encompasses a developmental gradient within a multicellular organism. Materials and MethodsThe Unigene set was selected from the expressed sequence tags (ESTs) presented in ref. 5, using cluster analysis. ESTs were transformed into Escherichia coli by using TSS competent cells (6), plasmids were prepared by using 96-well Multiscreen FB plates (Millipore), inserts were PCR amplified by using vectorspecific primers, and PCR products were purified on Multiscreen PCR filter plates (Millipore) and spotted in duplicate onto CMT GAPS slides (Corning) by using the GMS 417 Arrayer (Affymetrix, Santa Clara, CA) as described (7). All PCR products were checked on ethidium bromide-stained agarose gels. Nine clones giving double PCR bands were excluded from the analysis.A subset of 2,085 of the 2,995 PCR products in the Unigene set...

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Identification of the SAAT Gene Involved in Strawberry Flavor Biogenesis by Use of DNA Microarrays

Cited by 84 publications

References 0 publications

Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)

Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)

The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures

A transcriptional roadmap to wood formation

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