Network Analyses Reveal Shifts in Transcript Profiles and Metabolites That Accompany the Expression of SUN and an Elongated Tomato Fruit

Abstract

SUN controls elongated tomato (Solanum lycopersicum) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression of SUN. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterningrelated processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.

Nitric Oxide Overproduction in Tomato shr Mutant Shifts Metabolic Profiles and Suppresses Fruit Growth and Ripening

“…While shr had 64 unique interaction pairs and lost 485 interaction pairs present in the WT, sun fruits had 151 unique interaction pairs and lost 273 interaction pairs. Consistent with SUN being a protein with calmodulin recruitment domains, the mutation in it affects the calcium related processes; the major metabolic shifts in sun mutant were related to calcium signaling (Clevenger et al, 2015). Likewise, it can be assumed that analogous to sun mutant, the metabolic shifts in shr mutant may be related to its modulation of NO level.…”

“…Similar to shr mutant, tomato sun mutant also showed massive shifts in metabolite interactions, with the loss of several interactions and appearance of unique interactions compared to WT (Clevenger et al, 2015). While shr had 64 unique interaction pairs and lost 485 interaction pairs present in the WT, sun fruits had 151 unique interaction pairs and lost 273 interaction pairs.…”

A Comparison of sun, ovate, fs8.1 and Auxin Application on Tomato Fruit Shape and Gene Expression

“…To compare the fruit shape among different NILs and auxin treatments, principal component analysis (PCA) was conducted using the prcomp() function in R with the 9 specific fruit shape attributes mentioned above. Before performing the PCA, data were mean centered and converted to their Z-score as described by Clevenger et al (2015). Visualization of the PCA result was conducted using ggplot() in R.…”

“…Gene expression value calculation and PCA. Illumina reads filtration, alignment and expression value calculation were carried out according to Huang et al (2013) and Clevenger et al (2015) by using Heinz1706 SL2.50 genome as reference. Gene expression value was represented as reads per kilobase of exon model per million mapped reads (RPKM).…”

In silico Transcriptional Regulatory Networks Involved in Tomato Fruit Ripening

“…In this context, in silico analysis of large gene expression datasets has been used in the recent years in order to construct gene regulatory networks (Pan et al, 2013; Clevenger et al, 2015). …”