Enriched GO terms among genes differentially expressed in abscission zone after 3 h ethylene treatment.

<p>A Cytoscape view of enriched GO terms in BinGO where categories in GoSlimPlants (Maere <i>et al</i>., 2005) were used to simplify the analysis. The color bar shows the statistical significance, with enrichment significance level <i>P</i><0.05, and the false discovery rate <i>FDR</i> <0.05. The size of the node is proportional to the number of genes in the GO category. The pin-like symbols indicate enriched GO terms specifically in the abscission zone relative to the basal portion and the apical portion.</p

List of abscission zone-specific transcription factors.

1<p>Best Arabidopsis homolog if not functional studied in tomato; See text for tomato gene details.</p

Transcriptome Analysis of Tomato Flower Pedicel Tissues Reveals Abscission Zone-Specific Modulation of Key Meristem Activity Genes

<div><p>Tomato flower abscises at the anatomically distinct abscission zone that separates the pedicel into basal and apical portions. During abscission, cell separation occurs only at the abscission zone indicating distinctive molecular regulation in its cells. We conducted a transcriptome analysis of tomato pedicel tissues during ethylene promoted abscission. We found that the abscission zone was the most active site with the largest set of differentially expressed genes when compared with basal and apical portions. Gene Ontology analyses revealed enriched transcription regulation and hydrolase activities in the abscission zone. We also demonstrate coordinated responses of hormone and cell wall related genes. Besides, a number of ESTs representing homologs of key Arabidopsis shoot apical meristem activity genes were found to be preferentially expressed in the abscission zone, including <em>WUSCHEL</em> (<em>WUS</em>), <em>KNAT6</em>, <em>LATERAL ORGAN BOUNDARIES DOMAIN PROTEIN 1</em>(<em>LBD1</em>), and <em>BELL</em>-like homeodomain protein 1 (<em>BLH1</em>), as well as tomato axillary meristem genes <em>BLIND</em> (<em>Bl</em>) and <em>LATERAL SUPPRESSOR</em> (<em>Ls</em>). More interestingly, the homologs of <em>WUS</em> and the potential functional partner <em>OVATE FAMILIY PROTEIN</em> (<em>OFP</em>) were subsequently down regulated during abscission while <em>Bl</em> and <em>AGL12</em> were continuously and specifically induced in the abscission zone. The expression patterns of meristem activity genes corroborate the idea that cells of the abscission zone confer meristem-like nature and coincide with the course of abscission and post-abscission cell differentiation. Our data therefore propose a possible regulatory scheme in tomato involving meristem genes that may be required not only for the abscission zone development, but also for abscission.</p> </div

Response of ethylene related genes.

<p>Induction of (A) the ethylene receptor <i>LeETR6</i>, (B) ethylene biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase gene (<i>ACO1</i>), and (C-D) two ERF transcription factors during ethylene-promoted abscission.</p

Coordinated expression of auxin and other hormone related genes.

<p>Note the formation of distal to proximal gradient expression pattern for <i>GH3.3</i> (A), <i>TCP</i> (B), and <i>DWF4</i> (F). <i>GA 20ox-3</i> (C), <i>AOS</i> (D), and <i>ABA 8′-hydoxylase</i> (E) genes were most highly expressed in the abscission zone during abscission.</p

Induction of transcription factor genes during abscission.

<p>(A) <i>Blind</i> is specifically expressed in the abscission zone and is further induced significantly during the course of abscission. (B-E) <i>De novo</i> significant induction of four transcription factors.</p

Repression of meristem activity genes during abscission.

<p>Homologs of <i>WUS</i> (A) and <i>OVATE</i> (B) are specifically repressed in the abscission zone. <i>STM</i> (C) and <i>AS1</i> (D) were repressed in the abscission zone, but also in one or more additional tissues. E–F show the repression of the <i>SPL3</i> homolog and the tomato <i>MC</i> gene, a putative ortholog of the Antirrhinum <i>SQUAMOSA</i> gene.</p

Transcriptome responses of different tissues of tomato pedicels during ethylene-promoted abscission.

<p>A, The total numbers of genes differentially expressed (fold changes ≥2, 4, 8; <i>p</i><0.05) at 3 h and/or 6 h after ethylene treatment. B, Venn diagram showing the overlapping of differentially expressed genes in the abscission zone and flanking tissues (the basal portion and the apical portion). Lists of genes in each tissue are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055238#pone.0055238.s005" target="_blank">Tables S3</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055238#pone.0055238.s006" target="_blank">S4</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055238#pone.0055238.s007" target="_blank">S5</a>.</p

Data_Sheet_1_Functional characterization of the Serine acetyltransferase family genes uncovers the diversification and conservation of cysteine biosynthesis in tomato.PDF

Sulfur-containing compounds are essential for plant development and environmental adaptation, and closely related to the flavor and nutrition of the agricultural products. Cysteine, the first organic sulfur-containing molecule generated in plants, is the precursor for most of these active substances. Serine acetyltransferase (SERAT) catalyzes the rate-limiting step of its formation. However, despite their importance, systematic analyses of these enzymes in individual species, especially in economically important crops, are still limited. Here, The SERAT members (SlSERATs, four in total) were identified and characterized in tomato. Phylogenetically, the four SlSERAT proteins were classified into three subgroups with distinct genomic structures and subcellular localizations. On the function, it was interesting to find that SlSERAT3;1, possessed a high ability to catalyze the formation of OAS, even though it contained a long C-terminus. However, it retained the essential C-terminal Ile, which seems to be a characteristic feature of SERAT3 subfamily members in Solanaceae. Besides, SlSERAT1;1 and SlSERAT2;2 also had high activity levels and their catalyzing abilities were significantly improved by the addition of an OAS-(thiol)-lyase protein. At the transcriptional level, the four SlSERAT genes had distinct expression patterns during tomato plant development. Under abiotic stress conditions, the chloroplast-localized SlSERATs were the main responders, and the SlSERATs adopted different strategies to cope with osmotic, ion toxicity and other stresses. Finally, analyses in the loss-of-function and overexpression lines of SlSERAT1;1 suggested that function redundancy existed in the tomato SERAT members, and the tomato SERAT member was ideal target for S-assimilation manipulating in molecular breeding.</p