Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2005
Publication Date: 11/10/2005
Citation: Alba, R., Payton, P.R., Fei, Z., Debbie, P., Martin, G., Tanksley, S., Giovannoni, J.J. 2005. Transcriptome and selected metabolite analysis reveal multiple points of ethylene control during tomato fruit development. The Plant Cell. 17:2954-2965. Interpretive Summary: Fruit are unique to flowering plants and confer selective advantage to these species by aiding seed maturation and dispersal. The nutrients and colorful pigments contained in many fleshy fruit have been selected for this purpose through both evolution and domestication. Fleshy fruit are rich in flavor compounds, fiber, vitamins, and antioxidants, and are integral components of animal diets (including humans). This biological and dietary significance has made the molecular dissection of fruit maturation and ripening an area of considerable research interest. Despite this interest, little is known about transcriptome dynamics during expansion, maturation, or ripening of climacteric fruit. Here, we identify 869 genes that are related to tomato fruit development, show that nearly half of these genes are regulated by the ripening hormone ethylene, and show that transcript accumulation is extensively coordinated in tomato fruit. We show that ethylene regulates biochemistry, morphology, and gene expression throughout fruit development. Finally, comparison of expression patterns for genes encoding enzymes in fruit development pathways to the measured products of said pathways (e.g. ethylene, carotenoids, and vitamin C) suggests novel fruit development regulatory points influenced by ethylene.
Technical Abstract: Transcriptome profiling via cDNA microarray analysis identifies 869 genes that are differentially expressed in developing tomato pericarp. Parallel phenotypic and targeted metabolite comparisons were employed to inform the expression analysis. Transcript accumulation in tomato fruit was observed to be extensively coordinated and often completely dependent on ethylene. Mutation of an ethylene receptor (NEVER-RIPE; NR), which reduces ethylene sensitivity and inhibits ripening, alters the expression of 37% of these 869 genes. NR also influences fruit morphology, seed number, ascorbate accumulation, carotenoid biosynthesis, ethylene evolution and the expression of many genes during fruit maturation, indicating that ethylene governs multiple aspects of development both prior to and during fruit ripening in tomato. 628 of the 869 genes identified share homology (E-value below 1-10 x -11) with known gene products or known protein domains. 72 of these 628 loci share homology with previously described signal transduction or transcription factors, suggesting complex regulatory control. These results demonstrate multiple points of ethylene regulatory control during tomato fruit development and provide new insights to the molecular basis of ethylene-mediated ripening phenomena.