The regulatory mechanism of fruit ripening revealed by analyses of direct targets of the tomato MADS-box transcription factor RIPENING INHIBITOR

Figures & data

Figure 1. The rin mutation inhibits tomato fruit ripening. Wild type tomato fruits turn red and soften at the ripening stage (left), whereas the rin mutant fruits do not exhibit these changes (right). The rin mutation also inhibits the ripening-associated ethylene production and rise in respiration rate.¹⁴ The induction of RIN at the onset of ripening is not influenced by exogenous ethylene.³ In addition, the rin fruits show induction of some ethylene-responsive genes but do not ripen in response to exposure to exogenous ethylene,¹⁴ suggesting that RIN is required for both ethylene-dependent and independent pathways.²

Table 1. Overrepresented GO categories in the direct RIN target genes

GO ID	Category^1)	GO term	Positively-regulated (135 annotated genes)		Tomato genome (28,638 annotated genes)		P value	Examples of the classified direct RIN target genes
			Classified genes	ratio (%)	Classified genes	ratio (%)
GO:0009816	P	Defense response to bacterium, incompatible interaction	5	3.70	62	0.22	1.6E-05	GSH, LOXs, OSMs
GO:0051707	P	Response to other organism	5	3.70	97	0.34	1.2E-04	LOX, OSMs, UGTs
GO:0008898	F	Homocysteine S-methyltransferase activity	2	1.48	3	0.01	2.2E-04	HMTs
GO:0009611	P	Response to wounding	7	5.19	259	0.90	2.7E-04	C4H, 4CL, GH3, LOXs
GO:0009693	P	Ethylene biosynthetic process	4	2.96	29	0.10	1.7E-05	ACO6, ACS2, ACS4, E8
GO:0009908	P	Flower development ^2)	5	3.70	129	0.45	4.3E-04	AP2a, CNR, GSH, NAP, RIN
GO:0016165	F	Lipoxygenase activity	3	2.22	33	0.12	6.4E-04	LOXs
GO:0040007	P	Growth	3	2.22	35	0.12	7.6E-04	C4H, LOXs
GO ID	Category	GO term	Negatively-regulated (101 annotated genes)		Tomato genome (28,638 annotated genes)		P value	Examples of the classified direct RIN target genes
			Classified genes	Ratio (%)	Classified genes	Ratio (%)
GO:0003700	F	Sequence-specific DNA-binding transcription factor activity	17	16.83	1955	6.83	4.9.E-04	AP2s, HBs, IAAs, RAPs, WRKY
GO:0010093	P	Specification of floral organ identity	2	1.98	11	0.04	9.3.E-04	AP2s

A similarity-based functional annotation of tomato predicted genes was conducted using the Arabidopsis protein database with gene ontology (GO) information provided by the Arabidopsis Information Resource (TAIR), as previously reported.⁶ Shown are the subcategories in which the ratio of classified genes was significantly (p < 0.001 by Fisher's exact test) higher in the sets of direct RIN target genes than that in the tomato genome. Gene symbols and products: ACO6, 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase 6; ACS2, ACC synthase 2; ACS4, ACC synthase 4; AP2, APETALA2 homolog; AP2a, APETALA2a; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate:coenzyme A ligase; CNR, COLORLESS NON RIPENING; E8, ripening-associated ACO homolog; GH3, auxin-responsive GH3 family protein; GSH, glutamate-cysteine ligase; HB, homoebox protein; HMT, homocysteine S-methyltransferase; IAA, auxin/indole-3-acetic acid (AUX/IAA) transcriptional regulator family protein; LOX, lipoxygenase; NAP, NAC family transcription factor protein; OSM, osmotin-like protein; RAP, related to AP2/ERF family protein; RIN, RIPENING INHIBITOR; UGT, uridine diphosphate (UDP)-glucosyl transferase; WRKY, WRKY family transcription factor protein. (1) F and P indicate molecular function and biological process, respectively. (2) Tomato genes involved in fruit ripening regulation (AP2a, CNR and RIN) were categorized in “Flower development” because their Arabidopsis homologs are included in this category.

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