Network Inference Analysis Identifies an APRR2-Like Gene Linked to Pigment Accumulation in Tomato and Pepper Fruits    

Abstract

Carotenoids represent some of the most important secondary metabolites in the human diet, and tomato (Solanum lycopersicum) is a rich source of these health-promoting compounds. In this work, a novel and fruit-related regulator of pigment accumulation in tomato has been identified by artificial neural network inference analysis and its function validated in transgenic plants. A tomato fruit gene regulatory network was generated using artificial neural network inference analysis and transcription factor gene expression profiles derived from fruits sampled at various points during development and ripening. One of the transcription factor gene expression profiles with a sequence related to an Arabidopsis (Arabidopsis thaliana) ARABIDOPSIS PSEUDO RESPONSE REGULATOR2-LIKE gene (APRR2-Like) was up-regulated at the breaker stage in wild-type tomato fruits and, when overexpressed in transgenic lines, increased plastid number, area, and pigment content, enhancing the levels of chlorophyll in immature unripe fruits and carotenoids in red ripe fruits. Analysis of the transcriptome of transgenic lines overexpressing the tomato APPR2-Like gene revealed up-regulation of several ripening-related genes in the overexpression lines, providing a link between the expression of this tomato gene and the ripening process. A putative ortholog of the tomato APPR2-Like gene in sweet pepper (Capsicum annuum) was associated with pigment accumulation in fruit tissues. We conclude that the function of this gene is conserved across taxa and that it encodes a protein that has an important role in ripening.

Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening

“…These proteins might represent conserved genetic regulators that are shared among climacteric and non-climacteric fruits. Additional tomato transcription factor genes, including TOMATO AGAMOUS-LIKE1 (TAGL1), HD-ZIP HOMEOBOX PROTEIN-1 (HB-1), APETALA2a (AP2a), ETHYLENE RESPONSE FACTOR6 (ERF6), ARABIDOPSIS PSEUDO RESPONSE REGULATOR2-LIKE (APRR2-Like), and two FRUITFULL homologs (TDR4/ FUL1 and MBP7/FUL2), have been demonstrated to play vital roles in fruit ripening [13][14][15][16][17][18][19][20][21][22]. Recently, it was proposed that DNA methylation contributes to the regulation of fruit ripening [12,23], and the methylomes of tomato fruits from immature to fully ripe were profiled [23].…”

Ripening of Tomato Fruit and Susceptibility to Botrytis cinerea

“…cinerea interactions. A Golden2-like (SlGLK2) and KNOX (SlTKN4 and SlTKN2) transcription factors and a response-regulator factor (SlAPRR2-like) regulate chloroplast development and chlorophyll accumulation prior to the onset of ripening Pan et al 2013 ;Nadakudti et al 2014 ;Nguyen et al 2014 ). SlGLK2 over-expression apparently favors B. cinerea infections of unripe fruit, hypothetically because of the increased sugar contents of the fruit (A.L.T.…”

The wheat NB‐LRR gene TaRCR1 is required for host defence response to the necrotrophic fungal pathogen Rhizoctonia cerealis

“…An Artificial Neural Network (ANN) analysis on transcriptomic data has been used successfully to identify regulators of developmental processes in plants (Pan et al ., 2013). In our laboratory, comparative transcriptomics based on microarray or RNA‐seq analysis have been used to identify genes expressed differentially between sharp eyespot‐resistant wheat CI12633 and susceptible wheat Wenmai 6 following infection with R. cerealis .…”