a tomato vacuolar invertase inhibitor mediates sucrose ......2016/09/30 · a tomato vacuolar...
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A Tomato Vacuolar Invertase Inhibitor Mediates Sucrose Metabolism and Influences 1 Fruit Ripening 2 3
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Guozheng Qin2, Zhu Zhu2, Weihao Wang, Jianghua Cai, Yong Chen, Li Li, Shiping 5
Tian* 6
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Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 8
Nanxincun, Xiangshan, Haidian District, Beijing 100093, China (G.Q., Z.Z., W.W., J.C., Y.C., 9
S.T.); University of Chinese Academy of Sciences, Yuquanlu, Beijing 100049, China (W.W., 10
J.C., Y.C., S.T.); and Robert W. Holley Center for Agriculture and Health, Agricultural 11
Research Service, US Department of Agriculture, 14850 (L.L.). 12
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1 This work was supported by the National Natural Science Foundation of China (NSFC; 14
grant number 31530057 to S.T.), the National Basic Research Program of China (973 15
Program; grant number 2011CB100604 to S.T.), and the Youth Innovation Promotion 16
Association CAS (to G.Q.). 17
2 These authors contributed equally to the article. 18
* Address correspondence to [email protected]. 19
The author responsible for distribution of materials integral to the findings presented in this 20
article in accordance with the policy described in the Instructions for Authors 21
(www.plantphysiol.org) is: Shiping Tian ([email protected]). 22
S.T. and G.Q. designed research. G.Q. and W.W. carried out quantitative RT-PCR analysis, 23
ChIP assay, EMSA, and iTRAQ analysis. Z.Z. participated in overexpression and RNAi 24
vector construction, plant transformation, phenotype observation, lycopene and ethylene 25
measurements, enzyme assay, and Y2H. J.C. performed Western blot and protein localization 26
analysis. Y.C. participated in detection of sugar content. G.Q., Z.Z., W.W., L.L., and S.T. 27
analyzed data. G.Q., S.T., Z.Z., W.W. and L.L. wrote the paper. 28
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Short title: Regulation of fruit ripening by tomato SlVIF 30
ABSTRACT 31
Plant Physiology Preview. Published on September 30, 2016, as DOI:10.1104/pp.16.01269
Copyright 2016 by the American Society of Plant Biologists
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Fruit ripening is a complex process that involves a series of physiological and biochemical 32
changes that ultimately influence fruit quality traits, such as color and flavor. Sugar 33
metabolism is an important factor in ripening and there is evidence that it influences various 34
aspects of ripening, although the associated mechanism is not well understood. In this study, 35
we identified and analyzed the expression of 36 genes involved in sucrose metabolism in 36
ripening tomato (Solanum lycopersicum) fruit. Chromatin immunoprecipitation and gel 37
mobility shift assays indicated that SlVIF, which encodes a vacuolar invertase inhibitor, and 38
SlVI, encoding a vacuolar invertase, are directly regulated by the global fruit ripening 39
regulator RIN (RIPENING INHIBITOR). Moreover, we showed that SlVIF physically 40
interacts with SlVI to control sucrose metabolism. Repression of SlVIF by RNA interference 41
(RNAi) delayed tomato fruit ripening, while overexpression of SlVIF accelerated ripening, 42
with concomitant changes in lycopene production and ethylene biosynthesis. An iTRAQ 43
(isobaric tags for relative and absolute quantification)-based quantitative proteomic analysis 44
further indicated that the abundance of a set of proteins involved in fruit ripening was altered 45
by suppressing SlVIF expression, including proteins associated with lycopene generation and 46
ethylene synthesis. These findings provide evidence for the role of sucrose in promoting fruit 47
ripening and establish that SlVIF contributes to fruit quality and the RIN-mediated ripening 48
regulatory mechanisms, which are of significant agricultural value. 49
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INTRODUCTION 51
Fleshy fruit ripening is a complex process involving a series of physiological and 52
biochemical changes that influence fruit characteristics such as color, flavor, aroma and 53
texture (Giovannoni, 2004). Considerable progress has been made in elucidating the 54
biochemical and molecular basis of fruit ripening, including the discovery and 55
characterization of associated transcription factor networks and phytohormone signaling 56
pathways (Alba et al., 2005; Giovannoni, 2007; Klee and Giovannoni, 2011). As an example, 57
the MADS box transcription factor, RIPENING INHIBITOR (RIN) has been defined as a 58
global regulator of ripening, and has been shown to play a key role in modulating ethylene 59
biosynthesis, carbohydrate metabolism and aroma compound production (Vrebalov et al., 60
2002; Ito et al., 2008; Qin et al., 2012). Much current research into ripening focuses on the 61
identification of new candidate genes that affect fruit quality traits (Fujisawa et al., 2013; 62
Zhong et al., 2013), an important examples of which is flavor. 63
In general, fruit ripening is characterized by a substantial accumulation of 64
carbohydrates (Fraser et al., 1994) that provide energy for fruit development and contribute to 65
its flavor (Rolland et al., 2002; Zhu et al., 2013), thereby promoting consumption and seed 66
dispersal. Indeed, the content and composition of sugars largely determine fruit sweetness 67
and nutritional quality (Borsanie et al., 2009). Although the regulatory effects of sugars on 68
photosynthetic activity and plant metabolism have long been recognized (Godt and Roitsch, 69
1997; Koch, 2004; Kocal et al., 2008), the role of sugars as signaling molecules in fruit is less 70
understood. In many plant species, the major form of carbohydrate transported from the 71
leaves to the fruit is sucrose, which acts as an important form of energy storage/translocation 72
and plays a central role in the growth and development. There is also increasing evidence that 73
sucrose may play a non-nutritive role as a regulator of cellular metabolism, possibly by 74
altering gene expression (Huber and Huber, 1996; Rolland et al., 2002; Vaughn et al., 2002; 75
Ruan et al., 2010; Eveland and Jackson, 2012). Sucrose imported into fruits is degraded into 76
hexoses (glucose and fructose) for various metabolic and biosynthetic processes and 77
re-synthesized in the cytosol, vacuole and apoplast (Koch, 2004). Sucrose turnover in vivo is 78
catalyzed by sucrose synthase (SS) and invertase (Ruan et al., 2010). SS converts sucrose into 79
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UDP-glucose and fructose in the presence of UDP, whereas invertase hydrolyzes sucrose into 80
glucose and fructose in an irreversible reaction (Klann et al., 1996; Ruan et al., 2010). 81
Invertases play a major role in plant development and in responses to biotic and abiotic 82
stresses, and have been suggested to have important regulatory functions in carbon 83
metabolism and development in fruit (Jin et al., 2009). According to their subcellular 84
locations, invertases are classified as cell wall invertase (CWI), vacuolar invertase (VI), and 85
cytoplasmic invertase (CI) or neutral invertase (NI) forms (Sturm, 1999). In tomato fruit, 86
CWI activity is tightly linked with fruit sugar levels (Fridman et al., 2004), and is thought to 87
hydrolyze extracellular sucrose when the apoplastic pathway is active (Jin et al., 2009). Since 88
the vacuole is a storage organelle for sugars, VI is believed to modulate the sucrose/hexose 89
ratio in fruits. Antisense suppression of TIV1, a VI gene, in tomato was reported to result in 90
reduced hexose accumulation during fruit ripening (Klann et al., 1996). Similar findings were 91
reported in other fruits, such as grape (Vitis vinifera) berry (Davies and Robinson, 1996) and 92
muskmelon (Cucumis melo) (Yu et al., 2008), suggesting that VI controls the sugar 93
composition in broad range of fleshy fruit. Given the critical role of VI in fruit development 94
and ripening, its activity is likely to be tightly regulated in vivo. Studies have shown that the 95
invertase is regulated by a range of signals at the transcriptional level (Long et al., 2002; 96
Proels and Roitsch, 2009), and that invertase activity is controlled post-translationally by 97
inhibitor proteins (Hothorn et al., 2004). 98
Invertase inhibitors bind to invertases to form inactive complexes. Vacuolar invertase 99
inhibitors (VIF) have been isolated from tobacco (Nicotiana tabacum), Arabidopsis thaliana, 100
and potato (S. tuberosum) (Greiner et al., 1998; Link et al., 2004; Brummell et al., 2011). 101
Moreover, ectopic expression of Nt-inhh, a tobacco VIF, in potato tubers strongly reduced VI 102
activity and blocked hexose accumulation (Greiner et al., 1999), while heterologous 103
expression of recombinant potato VIF (INH2) suppressed potato VI activity in vitro 104
(Brummell et al., 2011). However, to our knowledge nothing has been reported regarding the 105
action or significance of fruit VIFs, which, if present, may be important for regulating VI 106
activity and hence the sugar composition of fruits. 107
Previous studies suggested a link between sugars and pigment metabolism in fleshy 108
fruit: in vitro sucrose supplementation promotes color changes in citrus (Citrus unshiu) fruit 109
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epicarp (Iglesias et al., 2001) and in tomato (Solanum lycopersicum) fruit pericarp discs 110
(Télef et al., 2006). However, evidence that the internal quality trait (sugar levels) and 111
external quality trait (color) of fruits are linked in vivo is lacking. Moreover, much remains to 112
be learnt about how sugars affect fruit quality traits and regulate ripening remains. In this 113
current study, we identified a set of genes involved in sucrose synthesis and degradation, 114
including VI and VIF, in tomato as direct targets of the ripening regulator, RIN. Our findings 115
indicate a role for sucrose in promoting pigment biosynthesis and fruit ripening in vivo, and 116
establish VIF as a novel genetic tool for regulating fruit ripening. 117
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RESULTS 120
Expression Analysis of Genes Involved in Sucrose Metabolism during Tomato Fruit 121
Ripening 122
The sucrose metabolic pathway is well-established; however, the expression profiles of 123
genes involved in this process during fruit ripening have not been well characterized. Sucrose 124
metabolism includes the degradation and re-synthesis of sucrose in the cytosol, vacuole and 125
apoplast. Several gene families are involved in these processes, including those encoding 126
invertase, invertase inhibitor, sucrose synthase, hexokinase, fructokinase, and sucrose 127
phosphate synthase (Carrari and Fernie, 2006) (Figure 1A). We identified the orthologs of 128
these genes in tomato in the SGN (SOL Genomics Network, http://solgenomics.net/) 129
databases using the reported gene sequence of each gene family from tomato, or another 130
Solanaceous species, as a query. A total of 36 genes were identified (Supplemental Table S1), 131
of which, 20 have previously been reported (Klann et al., 1992; Elliott et al., 1993; Wang et 132
al., 1993; Kanayama et al., 1997; Menu et al., 2001; Fridman and Zamir, 2003; Lunn and 133
MacRae, 2003; German et al., 2004; Kandel-Kfir et al., 2006; Jin et al., 2009; Goren et al., 134
2011; Li et al., 2012). The 16 unreported genes were named numerically, or on the basis of 135
the results of phylogenetic analysis. The expression of these 36 genes during ripening in 136
wild-type tomato, or in fruits at an equivalent stage, based on the number of days after 137
anthesis, in the rin mutant during fruit ripening was analyzed by quantitative RT-PCR, using 138
gene specific primers (Supplemental Table S2). To understand the temporal expression of 139
these sucrose metabolism related genes in the overall context of fruit ripening, the expression 140
of ripening marker genes (RIN, NOR, LePG, EXP1, ACS2, ACO1, PSY1, PDS) (Supplemental 141
Table S3) was also determined. 142
Eleven invertase genes were identified in the tomato genome, of which five are 143
predicted to encode CWI proteins (LIN5-9), one encodes a VI (VI), and five encode CI 144
(NI1-5). The expression of these genes had different patterns from each other in the rin 145
mutant during ripening (Figure 1B). Notably, LIN8, LIN9, NI2, and NI4 showed higher 146
expression levels in rin, whereas VI expression was significantly lower in the mutant 147
throughout ripening. 148
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The activity of invertase has been shown to be controlled post-translationally by 149
binding to inhibitor proteins (Hothorn et al., 2004), forming an inactive complex. Although 150
no inhibitor proteins were identified in the tomato genome for CI, one gene encoding an 151
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inhibitory protein, VIF, was found for VI and two inhibitors, CIF1 and CIF2, were identified 152
for CWI. The expression of VIF was higher in the fruit of rin mutant than in wild type, while 153
the opposite expression patterns were found for CIF1 and CIF2 (Figure 1B). These results 154
indicated that RIN promotes the expression of the VI gene and suppresses the expression of 155
its inhibitor. Conversely, RIN suppresses the expression of the CWI gene and promotes the 156
expression of its inhibitor. 157
Six sucrose synthase genes (SS1-7) were identified in the tomato genome, which 158
showed different patterns of gene expression from each other in the rin mutant at equivalent 159
days after anthesis, and the expression of SS6 was notably lower in the mutant throughout 160
ripening (Figure 1B). In addition, six hexokinase genes (HK1-6) and six fructokinase genes 161
(FK1-FKL2) were identified in the tomato genome. Their expression also showed different 162
patterns from each other in the rin mutant during ripening (Figure 1B), with the exception of 163
the fructokinase gene, FK4, whose expression has been specifically linked to stamen 164
development (German et al., 2002) and was not detected in this study. Lastly, four sucrose 165
phosphate synthase genes (SPSA1-SPSC) were identified, and their expression was shown to 166
be generally lower in rin mutant compared with wild type (Figure 1B). 167
168
ChIP-qPCR Analysis Reveals that RIN Directly Binds to the Promoters of Genes 169
Involved in Sucrose Metabolism 170
RIN regulates the expression of ripening-related genes, either directly or indirectly 171
(Fujisawa et al., 2013). To examine whether genes involved in sucrose metabolism are also 172
directly regulated by RIN, a chromatin immunoprecipitation (ChIP) assay was carried out. An 173
analysis of the promoter regions of the genes analyzed in this study identified varying 174
numbers of CArG-box binding motifs (Supplemental Table S1), which are elements that are 175
commonly found in MADS-box transcription factor binding sites (Ito et al., 2008). The 176
cross-linked DNA-protein complexes were immunoprecipitated with anti-RIN polyclonal 177
antibody that was prepared using a bacterial expressed recombinant RIN protein. To amplify 178
the promoter sequences surrounding the CArG-box binding sites from the 179
immunoprecipitated DNA, specific primers were designed (Supplemental Table S4), and the 180
binding of RIN to the promoter of ACC synthase 2 (ACS2), a known RIN-target gene (Ito et 181
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al., 2008), served as a positive control (Supplemental Figure S1). 182
ChIP screening using affinity-purified RIN antibodies, in combination with quantitative 183
PCR (ChIP-qPCR), resulted in an enrichment in the promoter regions of 16 genes compared 184
with when non-specific antibodies (pre-immune rabbit IgG) were used (Figure 2; 185
Supplemental Figure S2). Notably, RIN directly bound to the promoter of VI and VIF (Figure 186
2). Taken together with the gene expression analysis showing that VI expression was lower in 187
the rin mutant than in the wild type, while VIF expression was higher (Figure 1B), these data 188
suggest that RIN modulates sucrose degradation in the vacuole during fruit ripening. A 189
similar result was found for genes encoding CWIs, specifically LIN7 and LIN8, and the gene 190
encoding the inhibitory protein of CWI, CIF1 (Figure 2). However, while the expression of 191
LIN7 and LIN8 was up-regulated, the expression of CIF1 was down-regulated in the rin 192
mutant during fruit ripening (Figure 1B). This indicates that sucrose degradation associated 193
with CWI is inhibited by the RIN protein during fruit ripening. The ChIP-qPCR analysis also 194
showed that RIN directly bound to the promoter of NI2 and NI4 (Figure 2), which encodes CI. 195
Lastly, RIN was shown to bind directly to the promoter of several other genes involved in 196
sucrose metabolism, e.g. SS3, HK3, and SPSA1 (Supplemental Figure S2). 197
198
Gel Mobility Shift Assay Confirms that RIN Binds to the Promoters of Sucrose 199
Metabolic Genes 200
In order to confirm the binding ability of RIN to the promoter regions of genes 201
identified in the ChIP assay, an electrophoretic mobility shift assay (EMSA) was performed 202
with purified recombinant RIN protein. Specifically we examined the ability of RIN to bind 203
to double-stranded and biotin-labeled probes (Supplemental Table S5) for the genes shown in 204
Figure 2 (VI, VIF, LIN7, LIN8, CIF1, NI2, and NI4), which contained CArG-box motifs. For 205
each gene, a band shift was observed when the purified RIN protein was mixed with the 206
biotin-labeled probe (Figure 3). Formation of the DNA-protein complexes could be prevented 207
by addition of an excessive amount of the corresponding unlabeled probe, indicating specific 208
binding of RIN to the biotin-labeled probe. Based on the different extent of competition by 209
the unlabeled DNA fragment that was observed among these genes, we concluded that RIN 210
had different binding affinities for the promoters of the analyzed genes. 211
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212
Identification of SlVIF and Assessment of its Physical Interaction with VI 213
Having demonstrated that VI and VIF were directly regulated by RIN, the putative VI 214
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inhibitor gene, VIF, was chosen for further functional analysis. VIF genes have been cloned 215
from A. thaliana, tobacco (Nicotiana tabacum), and potato (S. tuberosum), and reported to 216
modulate sucrose metabolism (Link et al., 2004); however, little is known about the 217
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expression of VIF genes in tomato fruit or their roles in ripening. Tomato VIF (GenBank 218
accession no. KC007445; hereafter referred to as SlVIF) was cloned based on sequence 219
similarity to the N. tabacum VIF (AY145781). SlVIF showed 81% and 71% amino acid 220
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identity with NtVIF (Y12806) and StVIF (FJ810206), respectively (Supplemental Figure S3). 221
All deduced proteins contained the four conserved cysteine residues that are a hallmark of all 222
known plant invertase inhibitors (Rausch and Greiner, 2004). We observed that SlVIF was 223
expressed in both vegetative and reproductive organs, but at different levels (Figure 4A). 224
Notably, SlVIF mRNA levels were high in fruit, and SlVIF protein levels peaked at 38 days 225
post-anthesis (dpa) before dropping (Figure 4B), consistent with SlVIF transcript abundance. 226
To confirm that SlVIF indeed localizes in the vacuole, we transformed tomato with a 227
construct encoding SlVIF fused to a green fluorescent protein marker, (GFP):SlVIF, as well 228
as with a GFP only construct. When we imaged transgenic tomato root cells, we observed 229
that the GFP:SlVIF fusion protein produced a strong signal in the vacuole (Figure 4C), while, 230
the GFP only control displayed fluorescence throughout the cell (Figure 4C). 231
Recombinant SlVIF protein was purified and tested for its inhibitory activity against VI 232
extracted from 44 dpa tomato fruit, to confirm whether SlVIF indeed acts as a SlVI inhibitor. 233
As shown in Figure 5A, a decrease in the VI activity was observed upon increasing the SlVIF 234
concentration, while SlVIF had no inhibitory effects on CWI activity. To investigate whether 235
SlVIF physically interacted with SlVI, a yeast-2-hybrid (Y2H) assay was performed. The 236
cDNA fragments of SlVIF and SlVI were cloned into pGBKT7 (BD) and pGADT7 (AD) 237
vectors, respectively. The resulted plasmids, BD-SlVIF and AD-SlVI, were co-transformed 238
into yeast strains. Yeasts co-transformed with BD and AD (BD/AD), BD-SlVIF and AD 239
(BD-SlVIF/AD), and AD-SlVI and BD (AD-SlVI/BD) were used as controls. As shown in 240
Figure 5B, yeast co-transformed with BD-SlVIF and AD-SlVI displayed normal growth and 241
blue color on the selective SD/-Leu/-Trp/-His/-Ade (SD-LTHA) medium containing X-α-Gal, 242
whereas the controls showed no growth. Taken together, these results indicate that SlVIF 243
interacts with SlVI to suppress SlVI activity. 244
245
SlVIF Influences Sucrose Metabolism and Fruit Ripening 246
To examine the effects of SlVIF on sugar metabolism and fruit ripening, a 35S:SlVIF 247
overexpression construct and a SlVIF RNAi construct were separately introduced into tomato. 248
Three independent transgenic lines corresponding to each construct and containing 249
single-copy transgenes were identified by quantitative real-time PCR analyses (Mason et al., 250
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2002). The OE2 (SlVIF overexpression line 2) and S4 (SlVIF silenced line 4) lines with the 251
highest and lowest transcript level of SlVIF, respectively, were selected for further study. 252
Enzyme activity assays revealed that the VI activity was suppressed in fruit of the OE2 253
line, but elevated in fruit of the S4 line compared, with wild-type fruit at different ripening 254
stages (Figure 6A). CWI and NI activities were not affected by presence of the transgenes 255
(Figure 6B and 6C), confirming that SlVIF specifically inhibited VI activity. To investigate 256
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whether alteration of the SlVIF activity affected fruit sugar metabolism, levels of sucrose, 257
glucose, and fructose were measured. Overexpression of SlVIF resulted in 10-fold increase in 258
sucrose levels and a 40% decrease in hexose levels in 38 dpa OE2 fruits. In contrast, 259
silencing SlVIF led to lower sucrose levels and higher hexose levels than in the wild-type 260
control fruit (Figure 6D to 6F). These results demonstrated that SlVIF influenced sugar 261
metabolism and that altering its expression caused a substantial change in sucrose levels in 262
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fruits. 263
We noted that alteration of sucrose levels in the transgenic lines was accompanied by 264
changes in the onset of fruit ripening (Figure 6G). Fruit color changed from 35 dpa to 44 dpa 265
in wild-type fruit, but the color transition from green to red was faster in the OE2 line and 266
slower in the S4 line (Figure 6G). Moreover, we determined that while the red colored 267
carotenoid pigment, lycopene, was detectable from 38 dpa in the wild-type fruit, it started to 268
accumulate in the OE2 line at 35 dpa, and continued to increase over time, whereas no 269
significant changes in lycopene levels were observed from 35 dpa to 38 dpa in fruit of the S4 270
line (Figure 6H). We concluded that altering sugar content affected carotenoid pigment 271
biosynthesis, which in turn affected the timing of the onset of ripening. We also observed that 272
overexpression of SlVIF led to a 60% increase of ethylene production at 35 dpa compared 273
with the control, and repression of SlVIF expression resulted in significant reduction in 274
ethylene production throughout the ripening process (Figure 6I), suggesting that the altered 275
sugar levels also affected phytohormone production to coordinately regulate fruit ripening. 276
To better understand the mechanism of action of SlVIF in ripening fruit, the transcript 277
levels of a set of ripening related marker genes (RIN, NOR, LePG, EXP1, ACS2, ACO1, PSY1 278
and PDS) were evaluated in SlVIF overexpressing and silenced tomato fruits by quantitative 279
RT-PCR (Figure 7). The results indicated that the expression levels of these ripening marker 280
genes were significantly influenced by SlVIF. Notably, the ripening regulators RIN and NOR 281
were repressed in the SlVIF RNAi fruits at 38 dpa and 41 dpa, but exhibited higher transcript 282
levels at 44 dpa compared with the wild type. This suggests that gene expression of RIN and 283
NOR was delayed in the SlVIF RNAi tomatoes during fruit ripening. 284
285
SlVIF Modulates the Expression of Ripening-Related Proteins 286
To further elucidate how SlVIF coordinately regulated fruit ripening, we performed an 287
isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic 288
analysis of wild-type and SlVIF RNAi fruit. Proteins were extracted from the frozen pericarp 289
tissue of wild-type and SlVIF RNAi fruits at 38 dpa and 41 dpa and labeled with 4-plex 290
iTRAQ reagents (Figure 8A). We analyzed three independent biological replicates, with a 291
replicate corresponding to tissue pooled from fruits from five different plants for each stage 292
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and each genotype. Using a S. lycopersicum protein database 293
(ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/), a 294
total of 4,240, 4,225, and 4,381 proteins were identified in both wild type and transgenic line 295
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in biological replicate 1, 2, and 3, respectively, with a global false discovery rate (FDR) < 1% 296
in each. A two-fold cut-off led to the identification of 185 and 203 proteins with significantly 297
altered levels in the SlVIF silenced fruits at 38 dpa and 41 dpa, respectively (Supplemental 298
Table S6). 299
The differentially expressed proteins identified at 38 dpa and 41 dpa were categorized 300
using Blast2go (https://www.blast2go.com/) into fourteen functional categories (Figure 8B). 301
Overall 139 of them were more abundant and 212 were less abundant, respectively, in the 302
transgenic fruit than in wide type (Figure 8C). We concluded that a set of ripening related 303
proteins were significantly affected by SlVIF expression (Figure 9). These included proteins 304
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involved in carotenoid biosynthesis, such as phytoene desaturase (PDS), in ethylene synthesis, 305
such as ACC oxidase 1 (ACO1) and peptide methionine sulfoxide reductase msrA (E4), and 306
in cell wall degradation, such as polygalacturonase A (LePG) and pectinesterase (PME). To 307
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determine whether the protein expression patterns correlated with transcript levels, 308
quantitative RT-PCR was carried out for the corresponding genes using gene specific primers 309
(Supplemental Table S7). Of the 15 genes analyzed, the expression of 12, including PDS, 310
CRTISO, ACO1, E4, and LePG, were consistent with the protein abundance variations 311
(Figure 9). These results further indicated that SlVIF affected the expression of 312
ripening-related genes. 313
314
315
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DISCUSSION 316
RIN Regulates Expression of Genes Involved in Sucrose Metabolism 317
Given the importance of the ripening process in determining the quality, taste and 318
aroma of fruit, considerable effort had been focused on understanding its control (Klee and 319
Giovannoni, 2011; Ecker, 2013). The MADS-box transcription factor, RIN, has been shown 320
to be a global regulator of fruit ripening (Vrebalov et al., 2002; Martel et al., 2011) and to be 321
critical for the production of characteristic tomato aromas derived from the LOX pathway 322
(Qin et al., 2012). However, the particular genes related to sugar metabolism and their 323
specific modulation by RIN have not been well defined. The VI, VIF, SS, HK, FK and SPS 324
gene families have been shown to be involved in sucrose metabolism by regulating the 325
degradation and re-synthesis of sucrose (Carrari and Fernie, 2006). Here, we identified a total 326
of 36 genes involved in sucrose metabolism in tomato (Supplemental Table S1) and analyzed 327
their expression in the wild type and the rin mutant by quantitative RT-PCR using gene 328
specific primers (Figure 1). Many of these genes were differentially expressed in the rin 329
mutant compared with the wild type at equivalent days after anthesis, including 11 invertase 330
genes (LIN5-9, VI, NI1-5), a VI inhibitor gene (VIF), 6 sucrose synthase genes (SS1-7), 4 331
sucrose phosphate synthase genes (SPSA1-SPSC) and 6 hexokinase genes (HK1-6). The data 332
suggest that RIN regulates sucrose metabolism during ripening by modulating the expression 333
of a specific set of genes that play crucial roles in sucrose degradation and re-synthesis. 334
Sugars have important hormone-like functions as primary messengers in signal 335
transduction, in addition to their essential roles as substrates in the carbon and energy 336
metabolism, and in polymer biosynthesis (Rolland et al., 2002). Following sucrose 337
degradation by SS and VI, the resulting hexoses undergo phosphorylation by FK and HK for 338
further metabolism (Claeyssen and Rivoal, 2007), suggesting that FK and HK are important 339
in hexose metabolism, hexose sensing and signaling (Eveland and Jackson, 2012). In this 340
study, we showed that RIN governs sugar metabolism via the regulation of a number of genes, 341
including SlVI and SlVIF, in the sucrose synthesis and degradation pathway (Figure 1B). SlVI 342
expression was lower in the rin mutant while that of SlVIF was higher, suggesting that RIN 343
can modulate sucrose degradation during fruit ripening via promoting SlVI expression and 344
suppressing its inhibitor SlVIF. Interestingly, the expression of RIN changed substantially in 345
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22
the SlVIF RNAi tomatoes during fruit ripening (Figure 7), suggesting that SlVIF affects RIN 346
expression via a positive feed-back loop. 347
348
SlVIF Functions on Sucrose Metabolism and Lycopene Synthesis 349
The deduced SlVIF sequence was shown to share a high homology with vacuolar 350
invertase inhibitors from tobacco and potato (Supplemental Figure S3). Four conserved 351
cysteine (Cys) residues were identified that, in a potato vacuolar invertase inhibitor, have 352
been shown to form disulfide bridges to stabilize the protein (Brummell et al., 2011). Gene 353
expression analysis showed that SlVIF was expressed in both vegetative and reproductive 354
organs (Figure 4A), and that its expression increased in fruit from 35 dpa to 44 dpa (Figure 355
4B), indicating that it is involved in fruit ripening. Greiner et al., (1999) suggested that the 356
homologous protein from tobacco, NtVIF, is vacuolar, because overexpression of NtVIF in 357
potato strongly inhibited VI but not CWI. This is consistent with our observation that 358
recombinant GFP-SlVIF fusion protein accumulated in the vacuole of tomato root cells 359
(Figure 4C). Overexpression of SlVIF in tomato reduced the activity of VI, whereas silencing 360
its expression resulted in increased VI activity (Figure 6A), indicating that invertase activity 361
is regulated by its endogenous inhibitor. Importantly, altered SlVIF expression did not affect 362
the activities of CWI or NI (Figure 6B and 6C), demonstrating the specificity of SlVIF for 363
SlVI. These results were further confirmed by Y2H analysis (Figure 5B). Previous reports 364
indicated a role for invertases and invertase inhibitors in mediating sugar levels in plants 365
(Greiner et al., 1999). Induction of the VIF expression in potato tubers contributes to 366
cold-induced sweetening resistance due to its inhibition of VI and resulting decrease in the 367
accumulation of reducing sugars (Brummell et al., 2011). Consistent with its predicted role, 368
overexpression of SlVIF in tomato fruits significantly inhibited sucrose hydrolysis, leading to 369
an increase in sucrose content and a reduction in hexose levels, while suppression of SlVIF 370
promoted sucrose hydrolysis and enhanced hexose levels (Figure 6D to 6F). 371
Post-translational regulation of enzymes involved in the sugar metabolic pathway 372
represents an important mechanism for regulating sugar levels and composition in plants 373
(Koch, 2004). Moreover, post-translational elevation of CWI activity by silencing of its 374
inhibitor has been shown to result in increased hexose accumulation in tomato fruits (Jin et al., 375
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23
2009), and a number of studies have shown that VI activity is correlated with hexose levels in 376
hexose-accumulating species of tomato (Miron and Schaffer 1991; Klann et al., 1996). 377
External sucrose supplementation was previously reported to promote a color break in citrus 378
(Citrus unshiu) and tomato fruit (Iglesias et al., 2001; Télef N, et al., 2006), indicating a link 379
between sugars and pigments. Color transition in tomato fruits is due to the degradation of 380
chlorophylls and the simultaneous accumulation of carotenoids, mainly lycopene, which is 381
affected by several factors (Giovannoni, 2004). However, evidence supporting a role for 382
sugars in pigment synthesis, and consequently fruit ripening, in vivo is still lacking. In this 383
study, overexpression of SlVIF in tomato decreased hexose content during ripening, in 384
contrast to fruits from wild-type and SlVIF RNAi plants (Figure 6E and 6F), suggesting a 385
connection between VI activity and hexose accumulation. Interestingly, altering sucrose 386
levels by modification of SlVIF expression resulted in a clear change in the timing of the 387
onset of fruit ripening. Specifically, the red transition was faster in fruit of the SlVIF 388
overexpressing line, but slower in the SlVIF RNAi line compared with the wild-type fruit 389
(Figure 6G), indicating that SlVIF plays a role in the regulation of sucrose metabolism and 390
pigment biosynthesis. 391
392
SlVIF Modulates Ethylene Production and the Expression of Ripening-Related Genes 393
Ethylene is thought to be required for the sucrose-induced modulation of carotenoid 394
accumulation in both climacteric and non-climacteric fruit (Iglesias et al., 2001; Télef et al., 395
2006), and ethylene production is concomitant with color change and lycopene biosynthesis, 396
which is an indicator of ripening in many climacteric fruit (Giovannoni, 2007). Suppression 397
of acid invertase expression can stimulate ethylene production in tomato and muskmelon fruit 398
(Klann et al., 1996; Yu et al., 2008), and we saw that overexpression of SlVIF in tomato 399
increased ethylene production (Figure 6I) and led to a precocious color shift, due to elevated 400
lycopene accumulation (Figure 6H). In contrast, ethylene production was decreased and fruit 401
coloring was delayed by silencing SlVIF in tomato (Figure 6G). This suggests that SlVIF is 402
involved in the regulation of ethylene production and fruit ripening. Using iTRAQ-based 403
quantitative proteomic analysis, we identified 185 and 203 proteins whose abundance was 404
significantly different in SlVIF silenced fruit compared with wild-type fruit at 38 dpa and 41 405
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24
dpa, respectively (Figure 8). Of these, 139 were more abundant in the transgenic fruit and 212 406
were less abundant (Figure 8C). Suppression of SlVIF expression affected the abundance of 407
many ripening-related proteins (Figure 9), including PDS, ACO1, E4, and LePG. Quantitative 408
RT-PCR analysis indicated that the expression levels of several ripening-related genes (PDS, 409
ACO1, E4, and LePG) were consistent with the corresponding protein abundance variations 410
(Figure 9). Altering sugar content and/or SlVIF expression also affected the abundance of 411
other ripening-related genes, suggesting a potential role for SlVIF in the regulation of fruit 412
ripening. Finally, ChIP-qPCR and EMSA assays showed that RIN directly bound to the 413
promoters of SlVI and SlVIF, along with those of 14 other genes involved in sucrose 414
metabolism (Figure 2 and 3; Supplemental Figure S2). These results indicate that RIN 415
controls sugar metabolism by modulating the expression of genes involved in sucrose 416
synthesis and degradation. 417
In conclusion, our study highlights an important role for SlVIF in fruit ripening and 418
establishes a link between sucrose metabolism, lycopene synthesis and ripening in tomato 419
fruit. Our results further suggest that SlVIF has potential value as a genetic tool to regulate 420
tomato fruit ripening through manipulating the interaction of VI and its inhibitor. 421
422
MATERIALS AND METHODS 423
Plant Materials and Growth Conditions 424
Tomato (Solanum lycopersicum cv. Ailsa Craig) plants were grown at 25°C with a 16-h 425
photoperiod. The flowers were tagged at anthesis to determine ripening-stages. For plants 426
grown in vitro, seeds were germinated on MS medium (Murashige and Skoog, 1962) with 16 427
h of light at 25°C and 8 h of darkness at 22°C. Seeds of the tomato mutant rin in the ‘Ailsa 428
Craig’ background were kindly provided by Dr. James J. Giovannoni (Boyce Thompson 429
Institute for Plant Research, Cornell University, Ithaca, NY). Fruit ripening stages used in 430
this study were 35, 38, 41 and 44 days post-anthesis (dpa). Fruits of rin or transgenic lines 431
were collected at the equivalent ripening stages determined by the number of dpa. 432
433
Identification of Tomato Genes Involved in Sucrose Metabolism 434
In order to identify tomato orthologs of genes involved in sucrose metabolism (i.e. 435
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25
genes encoding invertases, invertase inhibitors, sucrose synthases, sucrose phosphate 436
synthases, fructokinases and hexokinases), BLAST searches were carried out against the 437
NCBI (National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/) and 438
SGN (SOL Genomics Network, http://solgenomics.net/) databases using the reported gene 439
sequence as a query. The uniqueness of the identified genes was manually verified to remove 440
redundant sequences. GENSCAN (http://genscanw.biosino.org/) was used to predict the 441
putative open reading frames (ORFs) and proteins sequences. 442
443
Quantitative Real-Time PCR 444
Total RNA (2 μg) was extracted from pericarp tissues as described by Moore et al. 445
(2005). The extracted RNA was treated with DNase (Promega) and reverse-transcribed using 446
an oligo (dT)18 primer with Moloney murine leukemia virus (M-MLV) reverse transcriptase 447
(Promega) to synthesize cDNA. Quantitative real-time PCR (qRT-PCR) was performed with 448
Takara SYBR Green Master Mix and gene specific primers in a volume of 20 μL using an 449
Mx3000P system (Stratagene). The following condition was applied for PCR amplification: 450
95°C for 10 min, followed by 40 cycles of 95°C for 15 s and 60°C for 30 s. ACTIN 451
(BT012695) was used as an internal control, and the relative expression was calculated using 452
the comparative 2(−ΔCt) method (Schmittgen and Livak, 2008). Each experiment had three 453
biological repeats, each with three technical replicates. 454
455
Chromatin Immunoprecipitation (ChIP) Assay 456
ChIP assays were performed as previously described (Qin et al., 2012). Pericarp tissue 457
from 41 dpa fruit was collected and submerged in 1% formaldehyde under a vacuum to 458
cross-link genomic DNA and protein. Nuclei were enriched and then sonicated in nuclei 459
lysing buffer containing 50 mM Tris–HCl, pH 8.0, 10 mM EDTA, 1% SDS, 0.1 mM PMSF, 460
and proteinase inhibitors. The conditions for sonication were optimized to shear DNA to an 461
average size of 500~1,000 bp. A small aliquot of sonicated chromatin was reversely 462
cross-linked and served as the input DNA control. The remaining chromatin sample was 463
centrifuged at 16,000g for 5 min at 4°C, and the supernatant was diluted 10-fold in ChIP 464
dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl, pH 8.0, 167 mM 465
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26
NaCl, 0.1 mM PMSF, and proteinase inhibitors). Protein A-agarose/salmon sperm DNA 466
beads (Millipore) were used to preclear the chromatin solution for 1 h at 4°C. 467
Immunoprecipitation was carried out with affinity purified RIN polyclonal antibody (see 468
below), and the tube containing the samples were incubated on a rotator with gentle agitation 469
(25 rpm) for 12 h at 4°C. Reactions with preimmune serum IgG and without antibody were 470
used as negative and mock controls, respectively. Protein-chromatin immunocomplexes were 471
captured on Protein A-agarose beads by incubating at 4°C for 1 h. The beads were collected 472
by centrifugation at 16,000g for 2 min at 4°C, and the bead-bound immunocomplexes were 473
eluted with elution buffer (1% SDS, 0.1 M NaHCO3) by gently rotating for 15 min at 65°C. 474
The beads were collected and the supernatant (eluate) was transferred to a fresh tube. The 475
cross-linking of immunoprecipitated DNA was then reversed by incubation of the eluate in 476
0.2 M NaCl at 65°C overnight. The immunoprecipitated DNA was purified after Proteinase K 477
(Invitrogen, Carlsbad, CA, U.S.A.) treatment, and eluted in TE buffer (10 mM Tris-HCl, pH 478
8.0, 1 mM EDTA) before being used for PCR using the same conditions as for quantitative 479
RT-PCR analysis. The RIN binding sites (CArG-box) in the promoters of selected genes were 480
analyzed using PLACE Web Signal Scan (http://www.dna.affrc.go.jp/PLACE/signalup.html). 481
Primers used for PCR amplification are listed in Supplemental Table S4. 482
483
Electrophoretic Mobility Shift Assay (EMSA) 484
Recombinant His-tagged RIN protein was expressed in E. coli and purified as 485
previously described (Qin et al., 2012). The binding activity of RIN to specific DNA 486
sequences was assayed using a Lightshift Chemiluminescent EMSA kit (Thermo Scientific). 487
Briefly, purified RIN protein (1 μg) in a binding buffer containing 10 mM Tris-HCl (pH 7.2), 488
50 mM KCl, 1 mM DTT, 2.5% glycerol, 0.05% NP-40, and 50 ng μL-1 polydeoxy 489
(inosinate-cytidylate), was incubated for 20 min at room temperature in the presence or 490
absence of unlabeled (double-stranded) competitor probes. The 3' biotin end-labeled 491
double-stranded DNA probes, which were constructed by annealing complementary 492
oligonucleotides, were then added, and the incubation continued for 20 min. The sequences 493
of the biotin-labeled probes are listed in Supplemental Table S5. Protein-DNA complexes 494
were separated on 6% native polyacrylamide gels, and the biotin-labeled probes were 495
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27
detected according to the instructions provided with the EMSA kit. 496
497
Recombinant Protein Expression and Antibody Preparation 498
Recombinant RIN protein was prepared as previously described (Qin et al., 2012). For 499
recombinant SlVIF protein preparation, a SlVIF gene fragment without the predicted putative 500
vacuolar sorting sequence (SignalP 4.0) was amplified from tomato cDNA using primers 501
SlVIF-F (5’-GGTACCAACAACAACAACAACATCAT-3’) and SlVIF-R (5’-GAGCT 502
CTCATAATAACATTCTAATTA-3’). The fragments were digested using KpnI and SacI 503
and inserted into the pET30a vector (Merck KGaA, Darmstadt, Germany). The resulting 504
plasmid was transformed into Escherichia coli BL21 (Lys) cells, and expression of the 505
recombinant protein was induced by 1 mM of isopropyl-β-D-thiogalacto- pyranoside (IPTG). 506
Recombinant His-tagged proteins were purified using Ni-NTA His-Bind resin (Merck). 507
Antibodies were raised against the recombinant RIN and SlVIF proteins in New 508
Zealand White rabbits by AbMax Biotechnology Co.Ltd (Beijing, China). Polyclonal 509
antibodies were affinity-purified from antisera using AminoLink Plus coupling resin, 510
according to the manufacturer’s instructions (Thermo Scientific, 511
http://www.thermoscientific.com/). 512
513
Western Blot Analysis 514
Proteins were extracted from tomato fruit harvested at different ripening stages as in 515
Bate et al. (2004), fractionated on a 12% SDS-PAGE gel and electrotransferred to an 516
Immobilon-P PVDF membrane (Millipore). The membranes were blocked at 20°C for 2 h 517
with 5% BSA in PBS-Tween buffer (137 mM NaCl, 2.7 mM KCl, 8.1 mM NaH2PO4, 1.5 mM 518
KH2PO4 and 0.1% Tween-20, pH 7.4). Immunoblots were performed at 4°C overnight with 519
affinity-purified rabbit polyclonal anti-SlVIF as described by Wang et al. (2014). The 520
membranes were washed with PBS-Tween (3 × 10 min) and treated with the corresponding 521
secondary antibodies (Abmart) (1:5,000 dilutions) conjugated to horseradish peroxidase. 522
Immunoreactive bands were visualized using a chemiluminescence detection kit 523
(SuperSignal®, Pierce Biotechnology). As a protein control, an anti-GAPDH 524
(glyceraldehyde-3-phosphate dehydrogenase) (Abmart) immunoblot was used. Additionally, 525
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28
Coomassie brilliant blue staining was used as a loading control. 526
527
Plasmid Construction and Plant Transformation 528
To construct the 35S:GFP:SlVIF vector, the full-length SlVIF cDNA was inserted into a 529
GFP expression vector pCAMBIA2300. The SlVIF overexpression construct was made by 530
cloning the full-length SlVIF cDNA into the pBI121 vector (kindly provided by Dr. Jing Bo 531
Jin from Institute of Botany, the Chinese Academy of Sciences, Beijing, China) downstream 532
of the 35S promoter. 533
To construct the SlVIF RNAi plasmid, a 285 bp SlVIF fragment was amplified from 534
tomato cDNA (prepared from fruit pericarp at 35 dpa as described above) by the primer pair: 535
5’-TATAACACCGTCCTACGAGCCG-3’ and 5’-TCTTTATATCTGGTTC 536
ACGTAACG-3’. The resulting product was cloned into the PCR8/GW/TOPO Gateway entry 537
vector (Invitrogen). The cloned fragment was subsequently transferred into the destination 538
vector pK7GWIWG2 (Karimi et al., 2002) using the LR Clonase II enzyme (Invitrogen) 539
according to the manufacturer’s instructions. 540
The above constructs were individually transformed into Agrobacterium tumefaciens 541
strain GV3101 by electroporation. Tomato transformation was performed according to Fillatti 542
et al. (1987). The presence of transgenes in kanamycin resistant plants was confirmed by 543
PCR using a forward primer corresponding to the 35S promoter and a reverse primer specific 544
for SlVIF: 5’-CGGAAACCTCCTCGGATTCCATT-3’ and 5’-GGCTACCG 545
TTACATCGGCTCGTA-3’. 546
547
Invertase Activity and Inhibition Assays 548
The activities of VI, CWI and NI were assayed according to Miron and Schaffer (1991) 549
and Klann et al. (1993). Approximately 2 g of pericarp was homogenized in 10 mL of 550
extraction buffer containing 50 mM HEPES-NaOH (pH 7.5), 5 mM MgC12, 1 mM EDTA, 551
2.5 mM DTT, 10 mM ascorbic acid and 5 % polyvinyl-polypyrrolidone (PVPP). After 552
centrifugation at 20,000g for 30 min at 4°C, the supernatants were dialyzed for 16 h against 553
25 mM HEPES-NaOH (pH 7.5) and 0.5 mM EDTA and used as a crude enzyme extract for 554
VI and NI activity assays. The insoluble pellet was washed three times with extraction buffer 555
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29
and extracted for 1 hour with 10 mL of extraction buffer containing 1 M NaCl. After 556
centrifugation at 20,000g for 30 min at 4°C, the supernatants were dialyzed overnight and 557
used as crude enzyme extract for CWI assays. For VI and CWI activity assays, 0.2 mL of 558
enzyme extract was incubated for 30 min at 37°C with 0.6 mL of 100 mM sodium acetate 559
(pH 4.8) and 0.2 mL of 100 mM sucrose. Reactions were stopped by placing the reaction 560
tubes in boiling water for 5 min and reducing sugars were measured using dinitrosalicylic 561
acid (Sumner, 1921). NI activity was assayed in 50 mM HEPES-NaOH (pH 7.5) instead of 562
sodium acetate (pH 4.8). 563
For inhibition studies, VI or CWI enzyme preparations were mixed with recombinant 564
SlVIF protein, and incubated in the assay buffer for 30 min at 37°C prior to addition of 565
sucrose and measurement of enzyme activity. 566
567
Y-2-H Assay 568
To generate the vector system for the Y-2-H analysis, the SlVIF cDNA fragment 569
encoding the mature protein and the full-length cDNA of SlVI (Genbank accession no. 570
M81081) were cloned into the pGBKT7 (BD) and pGADT7 (AD) vectors (Clontech), using 571
specific primers (SlVIF: 5’-CGGAATTCAACAACAACAACAACATCAT-3’ and 572
5’-AACTGCAGTCATAATAACATTCTAATTATG-3’; SlVI: 573
5’-CGGAATTCATGGCCACTCAGTGTTATGA-3’ and 574
5’-CCGCTCGAGTTACAAGTCTTGCAAAGGGA-3’), resulting in the BD-SlVIF and 575
AD-SlVI plasmids. The two plasmids were co-transformed into the yeast strain 576
Saccharomyces cerevisiae AH109 according to the manufacturer’s instructions (Clontech), 577
and dripped on synthetic dropout nutrient medium SD-LT (SD/-Leu/-Trp) and SD-LTHA 578
(SD/-Leu/-Trp/-His/-Ade) containing X-α-Gal. As a control, BD and AD, BD-SlVIF and AD, 579
BD and AD-SlVI were also co-transformed and analyzed, respectively. 580
581
Sugar, Lycopene and Ethylene Measurements 582
Sugars were extracted and determined according to Zhu et al. (2013). 583
Pericarp lycopene content was measured as described by Choi and Huber (2008). 584
Tomato pericarp tissue samples (5 g) were homogenized for 1 min in 50 mL of hexane–585
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30
acetone–ethanol (2:1:1, v/v) wrapped in aluminum foil to exclude light, then 15 mL of water 586
was added and the samples were vortexed for 10 s. After allowing phase separation on ice, 587
the lycopene concentration was determined by measuring the absorbance of the organic phase 588
(hexane) at 503 nm. The lycopene content was calculated using the molar extinction 589
coefficient of 17.2 L mol−1 m−1 and expressed as μg g−1 fresh weight. Three independent 590
samples derived from five fruits at each ripening stage were used for lycopene measurements. 591
Ethylene production was determined according to Zhu et al. (2010). Fruit were 592
harvested at different ripening stages, weighed and transferred to 1 L gas-tight jars. The jars 593
were sealed and incubated at 25°C for 2 h, then 1 mL of gas sample was withdrawn from the 594
headspace with a syringe and injected into a gas chromatograph (SQ-206, Beijing, China), 595
equipped with an activated alumina column and a flame ionization detector. Three 596
independent samples derived from five fruits at each ripening stage were used for the 597
ethylene measurements. 598
599
Protein Isolation, iTRAQ Labeling, and NanoLC–MS/MS Analysis 600
Fruits were harvested at 38 dpa and 41 dpa and total cellular protein was extracted from 601
fruit pericarp tissue as described by Saravanan and Rose (2004). Proteins were solubilized in 602
a protein buffer consisting of 500 mM triethylammonium bicarbonate (TEAB) and 0.6% SDS 603
(w/v), pH 8.5, and the protein concentrations were determined using the Bradford method 604
(Bradford, 1976) with bovine serum albumin as a standard. Proteins from each sample were 605
reduced with 10 mM tris-(2-carboxyethyl) phosphine (TCEP), alkylated with 50 mM methyl 606
methanethiosulfonate (MMTS), and digested with 10 ng μL-1 trypsin using the filter-aided 607
sample preparation (FASP) method (Wiśniewski et al., 2009). The tryptic peptides were 608
labeled using the iTRAQ Reagents 4-plex Kit (Applied Biosystems, 609
http://www.appliedbiosystems.com/) according to the manufacturer’s protocol. Samples 610
taken from wild-type and SlVIF silenced tomatoes at 38 dpa were labeled with iTRAQ tags 611
116 and 114, respectively, while samples from wild-type and SlVIF silenced tomatoes at 41 612
dpa were labeled with iTRAQ tags 117 and 115, respectively. Three independent biological 613
replicates were analyzed. The iTRAQ-labeled samples were combined and then fractionated 614
with high-pH reversed-phase chromatography using the Agilent Technologies 1290 UPLC 615
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31
system. Briefly, the pooled iTRAQ-labeled peptides were reconstituted using buffer A (20 616
mM ammonium formate, pH 10, in water) and loaded onto a 4.6 × 250 mm, 150 Å size 617
Durashell C18 (L) column containing 5 μm particles (Agela Technologies). The peptides was 618
eluted at a flow rate of 0.8 ml min-1 with a gradient of 2% buffer B (20 mM ammonium 619
formate in 80% acetonitrile, pH 10) for 5 min, 2-30% buffer B for 25 min, and 30-90% buffer 620
B for 10 min. The system was maintained in 90% buffer B for 10 min and then equilibrated 621
with 2% buffer B for 10 min. The elution was monitored by measuring UV absorbance at 210 622
nm, and fractions were collected every 1 min. A total of 48 fractions were collected and 623
pooled into a total of 6 fractions. After reconstitution in formic acid, the labeled peptides 624
were desalted and submitted for NanoLC–MS/MS analysis. 625
The MS analysis was carried out using a NanoLC system (NanoLC–2D Ultra Plus, 626
Eksigent, http://www.eksigent.com/) equipped with a Triple TOF 5600 Plus mass 627
spectrometer (AB SCIEX, http://www.absciex.com/). The iTRAQ-labeled peptide mixtures 628
were desalted on a 100 μm× 20 mm trap column and eluted on an analytical 75 μm× 150 mm 629
column. Both the trap column and the analytical column were filled with the Magic C18-AQ 630
5 μm 200 Å phase (Michrom BIORESOURCES, Inc). Peptides were separated by a gradient 631
formed by 0.1% formic acid (mobile phase A) and 100% acetonitrile, 0.1% formic acid 632
(mobile phase B), from 5 to 30% of mobile phase B over 75 min at a flow rate of 300 nL/min. 633
The precursor ions were selected across the mass range of 350–1500 m/z. High resolution 634
mode (>30000) was applied using 250 ms accumulation time per spectrum. A maximum of 635
25 precursors per cycle from each MS spectrum were chosen for fragmentation with 100 ms 636
minimum accumulation time for each precursor and dynamic exclusion for 18 s. Tandem 637
mass spectra were recorded in high sensitivity mode (resolution >15000) with rolling 638
collision energy and iTRAQ reagent collision energy adjustment on. 639
Protein identification and quantification were performed using ProteinPilot™ 4.5 640
software (AB SCIEX), and database searches were carried out using the S. lycopersicum 641
protein database ITAG2.4_proteins_full_desc.fasta 642
(ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/). 643
The following parameters was applied: (i) Sample Type: iTRAQ 4-plex (Peptide Labeled); (ii) 644
Cysteine Alkylation: MMTS; (iii) Digestion: Trypsin; (iv) Instrument: TripleTOF 5600; (v) 645
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32
Species: None; (vi) Quantitate: Yes; (vii) Bias Correction: Yes; (viii) Background Correction: 646
Yes; (ix) Search Effort: Thorough; (x) FDR Analysis: Yes. The peptide for quantification was 647
automatically chosen by the Pro GroupTM algorithm (AB SCIEX) to calculate the reporter 648
peak area. The reverse database search method (Elias and Gygi, 2007) was used to estimate 649
the global FDR for peptide identification. Proteins identified below the 1% global FDR were 650
used to calculate the meaningful cut-off value with the experimental replicate method (Gan et 651
al., 2007). 652
653
Supplemental Data 654
The following supplemental materials are available. 655
Supplemental Figure S1. The binding ability of RIN to the promoter of ACS2 as revealed by 656
chromatin immunoprecipitation. 657
Supplemental Figure S2. Chromatin immunoprecipitation reveals the direct binding of RIN 658
to the promoters of genes involved in sucrose metabolism. 659
Supplemental Figure S3. Alignment of amino acid sequences of invertase inhibitors from 660
various plants. 661
Supplemental Table S1. Genes involved in sucrose metabolism. 662
Supplemental Table S2. Primers used in qRT-PCR analysis of sucrose metabolism genes. 663
Supplemental Table S3. Ripening marker genes used for qRT-PCR analysis in this study 664
Supplemental Table S4. Gene-specific primers used in ChIP-qPCR assay. 665
Supplemental Table S5. Primers used for probes of EMSA. 666
Supplemental Table S6. Identification of the differentially expressed proteins in the SlVIF 667
silenced tomato fruit (vif) using iTRAQ-based quantitative proteomic analysis. 668
Supplemental Table S7. Primers for qRT-PCR analysis of selected genes identified in 669
iTRAQ. 670
671
ACKNOWLEDGEMENTS 672
We are grateful to Dr. James J. Giovannoni (Boyce Thompson Institute for Plant Research, 673
Cornell University) for providing the tomato seeds of wild type (Ailsa Craig) and mutant rin 674
used in the study. We thank Dr. Jing Bo Jin (Institute of Botany, the Chinese Academy of 675
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33
Sciences) for providing pBI121 vector. We also thank Dr. Zhuang Lu for analysis of MS/MS. 676
677
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34
FIGURE LEGENDS 678
679
Figure 1. Expression of genes involved in sucrose metabolism during fruit ripening. A, 680
Diagram of sucrose metabolism in tomato (Solanum lycopersicum). LIN, cell wall invertase; 681
VI, vacuolar invertase; NI, cytoplasmic invertase; VIF, vacuolar invertase inhibitor; CIF, cell 682
wall invertase inhibitor; SS, sucrose synthase; HK, hexokinase; FK, fructokinase; SPS, 683
sucrose phosphate synthase. B, Expression analyses of genes involved in sucrose metabolism 684
during fruit ripening in the wild type (WT) and the rin mutant by quantitative RT-PCR. The 685
stages of fruit ripening include 35 days post-anthesis (dpa), 38 dpa, 41 dpa, and 44 dpa. The 686
gene transcript levels are normalized against the ACTIN gene, followed by normalization 687
against the WT at 35 dpa. Values are means ± SD of three independent experiments. The 688
expression of ripening marker genes is shown. RIN, ripening inhibitor; NOR, non-ripening; 689
LePG, polygalacturonase A; EXP1, expansin 1; ACS2, 1-aminocyclopropane-1-carboxylate 690
synthase 2; ACO1, 1-aminocyclopropane-1-carboxylate oxidase; PSY1, phytoene synthase 1; 691
PDS, phytoene desaturase. 692
693
Figure 2. Chromatin immunoprecipitation reveals direct binding of RIN to the promoters of 694
genes involved in sucrose metabolism. The promoter regions of the target genes are indicated. 695
Red boxes represent CArG box elements and numbers above the box indicate the position of 696
these motifs relative to the translational start site. The blue fragments with upper-case letters 697
represent the regions used for ChIP-qPCR. Values are the percentage of DNA fragments that 698
were co-immunoprecipitated with specific anti-RIN antibodies, or non-specific antibodies 699
(preimmune rabbit IgG) relative to the input DNA. Error bars represent the SD of three 700
independent experiments. VI, vacuolar invertase; VIF, vacuolar invertase inhibitor; LIN, cell 701
wall invertase; CIF, cell wall invertase inhibitor; NI, cytoplasmic invertase. 702
703
Figure 3. RIN binding to the regulatory regions of target genes revealed by electrophoretic 704
mobility shift assay. The promoter regions of the target genes are indicated. Red boxes 705
indicate CArG box elements in the promoter region and numbers above represent the position 706
of these motifs relative to the translational start site. The probe sequences used for EMSA for 707
https://plantphysiol.orgDownloaded on May 3, 2021. - Published by Copyright (c) 2020 American Society of Plant Biologists. All rights reserved.
35
each target gene are shown, with red letters representing the CArG box. The protein–DNA 708
complexes were separated on 6% native polyacrylamide gels. Triangles indicate the 709
increasing amounts (10×, 100×, or 1000×) of unlabeled probes used for competition. The 710
specific complexes formed are indicated by arrowheads. VI, vacuolar invertase; VIF, 711
vacuolar invertase inhibitor; LIN, cell wall invertase; CIF, cell wall invertase inhibitor; NI, 712
cytoplasmic invertase. 713
714
Figure 4. Characterization of tomato SlVIF. A, Quantitative RT-PCR analyses of SlVIF in 715
vegetative and reproductive tomato organs. The ACTIN gene was used as an internal control. 716
Values are the means of three biological replicates. Bars represent standard deviations. B, 717
Western blot analysis of SlVIF protein abundance during fruit ripening. Proteins were 718
isolated from fruit at 35 days post-anthesis (dpa), 38 dpa, 41 dpa, and 44 dpa. An 719
anti-GAPDH (glyceraldehyde-3-phosphate dehydrogenase) immunoblot was used as a 720
protein control. In addition, Coomassie brilliant blue staining was used as a loading control. 721
C, Subcellular localization of GFP:SlVIF fusion protein. I, II and III, stable expression of the 722
GFP:SlVIF fusion protein in tomato root cells, showing fluorescent signal in the vacuole. IV, 723
V, and VI, stable expression of GFP alone in tomato root cells, showing fluorescent signals 724
throughout the cell. I and IV show fluorescent images; II and V are the same images viewed 725
using bright-field microscopy. III and VI are overlays of fluorescent and bright field images. 726
Bar =10 μm. 727
728
Figure 5. Interactions between SlVIF and SlVI. A, Inhibitory effects of recombinant SlVIF 729
on tomato vacuolar invertase and cell wall invertase. Residual invertase activity was 730
measured after pre-incubation with 10 to 160 pmol of recombinant SlVIF. Sucrose 731
concentration in the assay was 20 mM. B, Interaction between SlVIF and vacuolar invertase 732
(SlVI) in yeast. BD and AD represent plasmids pGBKT7 and pGADT7, respectively. 733
Transformants were grown on selective medium SD-LT (SD/-Leu/-Trp) and SD-LTHA 734
(SD/-Leu/-Trp/-His/-Ade) containing X-α-Gal for blue color development. 735
736
Figure 6. Function of tomato SlVIF in sucrose metabolism and fruit ripening. Invertase 737
https://plantphysiol.orgDownloaded on May 3, 2021. - Published by Copyright (c) 2020 American Society of Plant Biologists. All rights reserved.
36
activity, sugar content, color change phenotype, lycopene content, and ethylene production in 738
fruit of SlVIF overexpressing line 2 (OE2), SlVIF silenced line 4 (S4) and wild type (WT) 739
were examined during fruit ripening. A, Vacuolar invertase (VI) activity. B, Cell wall 740
invertase (CWI) activity. C, Neutral invertase (NI) activity. D, Sucrose content. E, Glucose 741
content. F, Fructose content. G, Photos of fruit from transgenic lines and wild-type control. H, 742
Lycopene content. I, Ethylene production. Bars represent standard deviations of three 743
biological replicates. 744
745
Figure 7. Expression of ripening marker genes in SlVIF overexpressing and silenced tomato 746
(Solanum lycopersicum) fruits. The gene transcript levels were determined by quantitative 747
RT-PCR. Total RNA was extracted from pericarp tissues of SlVIF overexpressing line 2 748
(OE2), SlVIF silenced line 4 (S4) and wild type (WT) at 35 days post-anthesis (dpa), 38 dpa, 749
41 dpa, and 44 dpa. The gene transcript levels are normalized against the ACTIN gene, 750
followed by normalization against the WT at 35 dpa. Values are means ± SD of three 751
independent experiments. RIN, ripening inhibitor; NOR, non-ripening; LePG, 752
polygalacturonase A; EXP1, expansin 1; ACS2, 1-aminocyclopropane-1-carboxylate synthase 753
2; ACO1, 1-aminocyclopropane-1-carboxylate oxidase; PSY1, phytoene synthase 1; PDS, 754
phytoene desaturase. 755
756
Figure 8. Identification of differentially expressed proteins in SlVIF silenced tomato fruits by 757
iTRAQ-based quantitative proteomic analysis. A, Schematic diagram of the workflow used in 758
this study. Three sets of biological replicate samples from wild-type (WT) and SlVIF silenced 759
fruit (vif) at 38 days post-anthesis (dpa) and 41 dpa were analyzed by iTRAQ, using the 760
nanoLC-MS/MS workflow for examining proteome changes. B, GO categories of 761
differentially expressed proteins at 38 dpa or 41 dpa. C, Venn diagram of differentially 762
expressed proteins identified at 38 dpa and 41 dpa. The numbers of differentially abundant 763
proteins at each ripening stage are shown. 764
765
Figure 9. Quantitative proteomic analysis showing that ripening-related genes are affected by 766
SlVIF expression. The changes in protein abundance in the SlVIF silenced fruits (vif) at 38 767
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37
days post-anthesis (dpa) and 41 dpa are shown as the ratio between vif and wild type (WT). 768
The mRNA expression levels were measured by quantitative real-time PCR. Total RNA was 769
extracted from pericarp tissues of SlVIF silenced fruit (vif) and WT at 35 dpa, 38 dpa, 41 dpa, 770
and 44 dpa. The gene transcript levels were normalized against the ACTIN gene, followed by 771
normalization against the WT at 35 dpa. The changes in transcript levels at 38 dpa and 41 dpa 772
are shown. The results for both protein and mRNA expression are means ± SD from three 773
independent experiments. PDS, phytoene desaturase; CRTISO, carotenoid isomerase; ACO1, 774
1-aminocyclopropane-1-carboxylate oxidase; E4, peptide methionine sulfoxide reductase; E8, 775
1-aminocyclopropane-1-carboxylate oxidase-like protein; SAM1, S-adenosylmethionine 776
synthase 1; SAM3, S-adenosylmethionine synthase 3; LoxC, lipoxygenase; PAL, 777
phenylalanine ammonia-lyase; VI, vacuolar invertase; LePG, polygalacturonase A; MAN4, 778
mannan endo-1 4-beta-mannosidase; PME2.1, pectinesterase; EXPA4, expansin. 779
https://plantphysiol.orgDownloaded on May 3, 2021. - Published by Copyright (c) 2020 American Society of Plant Biologists. All rights reserved.
38
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Parsed CitationsAlba R, Payton P, Fei Z, McQuinn R, Debbie P, Martin GB, Tanksley SD, Giovannoni JJ (2005) Transcriptome and selectedmetabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17: 2954-2965.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Bate NJ, Niu X, Wang Y, Reimann KS, Helentjaris TG (2004) An invertase inhibitor from maize localizes to the embryo surroundingregion during early kernel development. Plant physiol 134: 246-254.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Borsanie J, Budde CO, Porrini L, Lauxmann MA, Lombardo VA, Murray R, Andreo CS, Drincovich MF, Lara MV (2009) Carbonmetabolism of peach fruit after harvest: changes in enzymes involved in organic acid and sugar level modifications. J Exp Bot 60:1823-1837.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle ofprotein-dye binding. Anal Biochem 72: 248-254.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Brummell DA, Chen RK, Harris JC, Zhang H, Hamiaux C, Kralicek AV, McKenzie MJ (2011) Induction of vacuolar invertase inhibitormRNA in potato tubers contributes to cold-induced sweetening resistance and includes spliced hybrid mRNA variants. J Exp Bot62: 3519-3534.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Carrari F, Fernie AR (2006) Metabolic regulation underlying tomato fruit development. J Exp Bot 57: 1883-1897.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Choi ST, Huber DJ (2008) Influence of aqueous 1-methylcyclopropene concentration, immersion duration, and solution longevityon the postharvest ripening of breaker-turning tomato (Solanum lycopersicum L.) fruit. Postharvest Biol Tec 49: 147-154.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Claeyssen E, Rivoal J (2007) Isozymes of plant hexokinase: occurrence, properties and functions. Phytochemistry 68: 709-731.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Davies C, Robinson SP (1996) Sugar accumulation in grape berries: cloning of two putative vacuolar invertase cDNAs and theirexpression in grapevine tissues. Plant Physiol 111: 275-283.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Ecker JR (2013) Epigenetic trigger for tomato ripening. Nat Biotechnol 31: 119-120.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by massspectrometry. Nat Methods 4: 207-214.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Elliott KJ, Butler WO, Dickinson CD, Konno Y, Vedvick TS, Fitzmaurice L, Mirkov TE (1993) Isolation and characterization of fruitvacuolar invertase genes from two tomato species and temporal differences in mRNA levels during fruit ripening. Plant Mol Biol21: 515-524.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Eveland AL, Jackson DP (2012) Sugars, signalling, and plant development. J Exp Bot 63: 3367-3377.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Fraser PD, Truesdale M, Bird CR, Schuch W, Bramley PM (1994) Carotenoid biosynthesis during tomato fruit development. Planthttps://plantphysiol.orgDownloaded on May 3, 2021. - Published by Copyright (c) 2020 American Society of Plant Biologists. All rights reserved.
Physiol 105: 405-413.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Fillatti JJ, Kiser J, Rose R, Comai L (1987) Efficient transfer of a glyphosate tolerance gene into tomato using a binaryAgrobacterium tumefaciens vector. Nat Biotechnol 5: 726-730.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Fridman E, Carrari F, Liu YS, Fernie AR, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecificintrogressions. Science 305: 1786-1789.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Fridman E, Zamir D (2003) Functional divergence of a syntenic invertase gene family in tomato, potato, and Arabidopsis. PlantPhysiol 131: 603-609.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
Fujisawa M, Nakano T, Shima Y, Ito Y (2013) A large-scale identification of direct targets of the tomato MADS box transcriptionfactor RIPENING INHIBITOR reveals the regulation of fruit ripening. Plant Cell 25: 371-386.
Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title
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