Table III.
Hub metabolites and genes involved in the regulatory network controlling metabolite levels in tomato fruit tissues AGI, Arabidopsis Genome Initiative number; TAIR, The Arabidopsis Information Resource.
| Spot ID | Tomato Unigene | BLASTX TAIR Best Hit
|
No. of Correlationsa with Each Functional Category
|
K-Meansf/ Group No. | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | AGI | P | Metabolite (Met) or BIN:
|
Met
|
17
|
21
|
22
|
27b
|
28c
|
29d
|
30
|
Total
|
|||
| Total No.e: | 42 | 31 | 15 | 4 | 89 | 6 | 137 | 14 | 338 | ||||||
| Hormone synthesis response (BIN 17) | |||||||||||||||
| 1.2.20.12 | SGN-U327450 | Auxin-responsive family protein | At2g46690 | 4E-29 | 0 | 1 | 1 | 1 | 4 | 1 | 10 | 1 | 19 | 5 | |
| 5.3.3.5 | SGN-U320280 | IAA27, phytochrome-associated protein 2 | At4g29080 | 3E-70 | 1 | 1 | 0 | 0 | 2 | 1 | 5 | 0 | 10 | 5 | |
| 8.4.11.13 | SGN-U314505 | 2-Oxoglutarate-dependent dioxygenase | At1g06620 | 1E-106 | 0 | 4 | 1 | 0 | 3 | 1 | 4 | 0 | 13 | 2 | |
| 6.1.16.20 | SGN-U314506 | 2-Oxoglutarate-dependent dioxygenase | At1g06620 | 8E-51 | 0 | 4 | 1 | 0 | 3 | 0 | 5 | 0 | 13 | 2 | |
| 6.2.3.14 | SGN-U316692 | ACC synthase 2 | At1g01480 | 0.0 | 0 | 1 | 2 | 1 | 2 | 1 | 15 | 1 | 23 | 5 | |
| 1.2.19.20 | SGN-U313853 | ERF3 | At1g50640 | 2E-30 | 0 | 2 | 0 | 0 | 6 | 0 | 5 | 1 | 14 | 4 | |
| 1.1.10.9 | SGN-U314559 | Lipoxygenase 1 (LOX1) | At1g55020 | 0.0 | 1 | 0 | 4 | 0 | 5 | 1 | 5 | 0 | 16 | 3 | |
| 1.2.8.13 | SGN-U313563 | DWARF1/DIMINUTO | At3g19820 | 0.0 | 0 | 3 | 1 | 0 | 5 | 0 | 3 | 0 | 12 | 1 | |
| Redox (BIN 21) | |||||||||||||||
| 1.3.14.20 | SGN-U317819 | Protein disulfide isomerase | At3g16110 | 1E-177 | 0 | 2 | 2 | 0 | 4 | 0 | 10 | 0 | 18 | 4 | |
| 1.1.10.5 | SGN-U315704 | Ascorbate peroxidase 2, cytosolic | At3g09640 | 1E-109 | 2 | 3 | 0 | 0 | 3 | 0 | 5 | 0 | 13 | 4 | |
| 4.1.8.12 | SGN-U312635 | Glutathione transferase | At1g78380 | 8E-86 | 1 | 3 | 1 | 1 | 4 | 1 | 12 | 1 | 24 | 4 | |
| Polyamines (BIN 22) | |||||||||||||||
| 2.3.3.9 | SGN-U319156 | Polyamine oxidase 1 | At5g13700 | 1E-136 | 0 | 2 | 1 | 0 | 3 | 1 | 11 | 1 | 19 | 5 | |
| Transcription factors (BIN 27.3) | |||||||||||||||
| 1.1.2.18 | SGN-U321056 | Homeobox-Leu zipper protein HAT22 | At4g37790 | 1E-81 | 0 | 1 | 1 | 1 | 2 | 0 | 4 | 1 | 10 | 1 | |
| 8.2.16.2 | SGN-U314473 | SEPALLATA1 (SEP1) RIN | At5g15800 | 6E-71 | 0 | 5 | 0 | 0 | 3 | 1 | 5 | 0 | 14 | 3 | |
| 8.2.9.17 | SGN-U317381 | NAC domain-containing protein (NAC2) | At3g15510 | 7E-90 | 0 | 6 | 1 | 0 | 3 | 1 | 4 | 0 | 15 | 2 | |
| 3.2.13.13 | SGN-U313171 | NAC domain-containing protein (NAP) | At1g69490 | 1E-84 | 1 | 3 | 2 | 1 | 2 | 1 | 14 | 1 | 25 | 3 | |
| 4.1.14.17 | SGN-U316694 | bZIP transcription factor (TAG2) | At5g06950 | 1E-119 | 0 | 5 | 1 | 0 | 2 | 1 | 5 | 0 | 14 | 4 | |
| 6.2.16.4 | SGN-U325786 | AP2 domain-containing transcription factor | At5g67190 | 2E-38 | 0 | 3 | 3 | 0 | 1 | 1 | 11 | 0 | 19 | 3 | |
| DNA methylation (BIN 28.1) | |||||||||||||||
| 2.2.4.1 | SGN-U323958 | DNA (cytosine-5)-methyltransferase | At4g13610 | 0.0 | 0 | 4 | 1 | 1 | 3 | 0 | 14 | 1 | 24 | 5 | |
| 2.3.13.15 | SGN-U319104 | Histone deacetylase complex ubunit Sin3 | At1g24190 | 1E-106 | 0 | 2 | 1 | 0 | 5 | 0 | 4 | 0 | 12 | 4 | |
| Regulation of protein activity (BINs 29.3, 29.4, 29.5) | |||||||||||||||
| 2.4.13.5 | SGN-U314101 | Molecular chaperone | At5g15450 | 0.0 | 0 | 5 | 1 | 0 | 4 | 0 | 4 | 0 | 14 | 4 | |
| 2.3.3.5 | SGN-U313747 | Vacuolar processing enzyme γ | At4g32940 | 0.0 | 0 | 2 | 1 | 0 | 2 | 0 | 10 | 1 | 16 | 4 | |
| 3.4.20.16 | SGN-U317938 | Protein-l-isoaspartate O-methyltransferase | At5g50240 | 2E-97 | 1 | 4 | 1 | 0 | 4 | 0 | 4 | 0 | 14 | 4 | |
| 4.1.18.5 | SGN-U315846 | CBL-interacting Ser/Thr protein kinase | At3g17510 | 1E-169 | 0 | 2 | 2 | 1 | 3 | 1 | 13 | 1 | 23 | 3 | |
| 2.2.6.17 | SGN-U326261 | Leu-rich repeat transmembrane protein kinase | At3g03770 | 1E-62 | 0 | 2 | 1 | 1 | 3 | 1 | 13 | 1 | 22 | 2 | |
| 4.2.18.5 | SGN-U318361 | Mitogen-activated protein kinase 9 | At3g18040 | 0.0 | 0 | 2 | 0 | 1 | 2 | 1 | 8 | 2 | 16 | 5 | |
| 7.1.18.4 | SGN-U313783 | Protein kinase | At5g14640 | 0.0 | 0 | 3 | 0 | 0 | 2 | 1 | 8 | 1 | 15 | 4 | |
| 6.2.8.6 | SGN-U324081 | Protein kinase | At1g16670 | 3E-94 | 1 | 3 | 3 | 1 | 3 | 2 | 12 | 1 | 26 | 3 | |
| 7.1.19.16 | SGN-U337694 | Protein kinase | At2g17220 | 1E-50 | 0 | 2 | 2 | 1 | 3 | 1 | 14 | 1 | 24 | 5 | |
| 1.1.18.14 | SGN-U316649 | Protein kinase | At5g24010 | 8E-85 | 0 | 3 | 0 | 1 | 2 | 1 | 6 | 1 | 14 | 5 | |
| 1.4.18.1 | SGN-U316516 | Wall-associated kinase 3 | At1g21240 | 1E-57 | 1 | 3 | 2 | 1 | 2 | 2 | 12 | 1 | 24 | 3 | |
| 3.2.6.6 | SGN-U317284 | Protein phosphatase 2C PPH1 | At4g27800 | 1E-133 | 0 | 2 | 2 | 1 | 2 | 1 | 9 | 2 | 19 | 4 | |
| 6.4.18.3 | SGN-U316275 | Protein kinase | At2g35050 | 0.0 | 0 | 2 | 2 | 1 | 2 | 1 | 12 | 1 | 21 | 3 | |
| 2.3.8.1 | SGN-U321058 | ABC1 family protein, kinase | At4g31390 | 1E-154 | 0 | 3 | 3 | 0 | 2 | 1 | 8 | 0 | 17 | 4 | |
| 3.1.20.18 | SGN-U313737 | Ser carboxypeptidase | At5g09640 | 1E-101 | 1 | 4 | 2 | 1 | 2 | 1 | 14 | 1 | 26 | 4 | |
| 5.3.19.8 | SGN-U331984 | Ser carboxypeptidase | At5g42240 | 9E-82 | 1 | 2 | 1 | 0 | 5 | 0 | 8 | 1 | 18 | 4 | |
| 5.2.6.10 | SGN-U316193 | 20S proteasome α subunit C1 | At3g22110 | 1E-115 | 0 | 2 | 1 | 0 | 1 | 2 | 10 | 1 | 17 | 3 | |
| 6.4.13.2 | SGN-U316057 | Aspartyl protease protein | At1g11910 | 0.0 | 0 | 2 | 0 | 0 | 7 | 0 | 6 | 1 | 16 | 3 | |
| 2.2.10.18 | SGN-U316933 | HSP20-like chaperone | At2g37570 | 0.0 | 1 | 4 | 1 | 0 | 7 | 0 | 4 | 0 | 17 | 4 | |
| Signaling (BIN 30) | |||||||||||||||
| 7.2.18.4 | SGN-U317690 | Inositol-1,4,5-trisP 5-phosphatase | At1g47510 | 1E-108 | 0 | 2 | 1 | 1 | 2 | 1 | 15 | 0 | 22 | 2 | |
| Metabolite | |||||||||||||||
| Choline | 2 | 1 | 2 | 0 | 2 | 0 | 3 | 0 | 10 | 3 | |||||
a
Metabolite and regulatory gene correlations were calculated using Pearson correlation coefficients (P < 0.001). Genes were classified in BINs according to MapMan classification (Thimm et al., 2004).
b
Transcription factors (BIN 27.3).
c
DNA methylation (BIN 28.1).
d
Regulation of protein activity (BINs 29.3, 29.4, 29.5).
e
Number of metabolites or genes significantly detected in each gene BIN.
f
Hub metabolites and genes were classified in five groups by K-means analysis according to Figure 9.