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Tomato Proteome Reveals Genes Involved in Fruit Ripening

NEW YORK (GenomeWeb) – Analyzing the nuclear proteome in tomato cells has revealed a role for several genes that encode E2 ubiquitin-conjugation enzymes in the fruit ripening process, researchers report in a study published last week in Genome Biology.

It is the first comprehensive study of proteins present in the nuclei of tomato cells at various points according to the scientists, led by Yuying Wang and Shiping Tian of the Chinese Academy of Sciences. Prior studies had characterized the expression profile of nuclear proteins using mRNA levels, but the authors said this did not always correlate with actual levels of the proteins, and that the proteome study complemented the expression profiles as tools to help better understand the molecular basis of ripening.

"Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening," the researchers said in their study. "These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening."

The scientists used an iTRAQ-based quantitative proteomic analysis to view nuclear proteome alteration during tomato ripening. They isolated proteins during several ripening stages, from "mature green" to "red ripe," and reported that the largest functional class of proteins was associated with cell signaling and transcription regulation.

As part of the study, the researchers showed that tomatoes with a gene variant coding for a ripening-inhibiting transcription factor, rin, exhibited altered expression levels in a set of genes encoding for E2 ubiquitin-conjugating enzymes. The ubiquitin proteasome system had previously been implicated in regulating the ripening process.

Using a virus-induced gene-silencing assay, the researchers were able to show that some of these ubiquitin-conjugating enzyme genes are involved in the regulation of fruit ripening. Silencing the E2 genes SlUBC32 and SlUBC41 resulted in altered coloring during the "orange" ripening stage of the tomato.

"To our knowledge, this is the first report for identifying specific E2s as regulators in fruit ripening," the researchers said.