Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology

Joung, Je-Gun; Corbett, Anthony; Fellman, Shanna Moore; Tieman, Denise M.; Klee, Harry J.; Giovannoni, James J.; Fei, Zhangjun

doi:10.1104/pp.109.145169

Cited by 148 publications

(117 citation statements)

References 64 publications

(66 reference statements)

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“…To identify differentially regulated metabolic pathways in AP2i-1-8 plants, we analyzed our microarray data using the Plant MetGenMAP database (Joung et al, 2009). Among the pathways identified, we found an overrepresentation of primary metabolic processes (see Supplemental Table 1 online).…”

Section: Ap2a Silenced Fruits Show Increased Accumulation Of Sugars Amentioning

confidence: 99%

Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening

et al. 2011

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Fruit ripening in tomato (Solanum lycopersicum) requires the coordination of both developmental cues as well as the plant hormone ethylene. Although the role of ethylene in mediating climacteric ripening has been established, knowledge regarding the developmental regulators that modulate the involvement of ethylene in tomato fruit ripening is still lacking. Here, we show that the tomato APETALA2a (AP2a) transcription factor regulates fruit ripening via regulation of ethylene biosynthesis and signaling. RNA interference (RNAi)-mediated repression of AP2a resulted in alterations in fruit shape, orange ripe fruits, and altered carotenoid accumulation. Microarray expression analyses of the ripe AP2 RNAi fruits showed altered expression of genes involved in various metabolic pathways, such as the phenylpropanoid and carotenoid pathways, as well as in hormone synthesis and perception. Genes involved in chromoplast differentiation and other ripening-associated processes were also differentially expressed, but softening and ethylene biosynthesis occurred in the transgenic plants. Ripening regulators RIPENING-INHIBITOR, NON-RIPENING, and COLORLESS NON-RIPENING (CNR) function upstream of AP2a and positively regulate its expression. In the pericarp of AP2 RNAi fruits, mRNA levels of CNR were elevated, indicating that AP2a and CNR are part of a negative feedback loop in the regulation of ripening. Moreover, we demonstrated that CNR binds to the promoter of AP2a in vitro.

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Section: Ap2a Silenced Fruits Show Increased Accumulation Of Sugars Amentioning

confidence: 99%

Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening

et al. 2011

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“…These include genes encoding for proteases, pectinases, expansins, and extensins and a high number of genes encoding for enzymes involved in primary or secondary metabolism. In order to identify changed metabolic pathways, we loaded the microarray data into the Plant MetGenMAP database (Joung et al, 2009). Several metabolic pathways that can be linked to ripening were revealed to be regulated by FUL1/2, including Glu degradation, carotenoid biosynthesis, and suberin biosynthesis.…”

Section: Microarray Analysis Increases the Insight Into The Role Of Fmentioning

confidence: 99%

The Tomato FRUITFULL Homologs TDR4/FUL1 and MBP7/FUL2 Regulate Ethylene-Independent Aspects of Fruit Ripening

Bemer

Karlova

Ballester³

et al. 2012

Plant Cell

289

276

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Tomato (Solanum lycopersicum) contains two close homologs of the Arabidopsis thaliana MADS domain transcription factor FRUITFULL (FUL), FUL1 (previously called TDR4) and FUL2 (previously MBP7). Both proteins interact with the ripening regulator RIPENING INHIBITOR (RIN) and are expressed during fruit ripening. To elucidate their function in tomato, we characterized single and double FUL1 and FUL2 knockdown lines. Whereas the single lines only showed very mild alterations in fruit pigmentation, the double silenced lines exhibited an orange-ripe fruit phenotype due to highly reduced lycopene levels, suggesting that FUL1 and FUL2 have a redundant function in fruit ripening. More detailed analyses of the phenotype, transcriptome, and metabolome of the fruits silenced for both FUL1 and FUL2 suggest that the genes are involved in cell wall modification, the production of cuticle components and volatiles, and glutamic acid (Glu) accumulation. Glu is responsible for the characteristic umami taste of the present-day cultivated tomato fruit. In contrast with previously identified ripening regulators, FUL1 and FUL2 do not regulate ethylene biosynthesis but influence ripening in an ethylene-independent manner. Our data combined with those of others suggest that FUL1/2 and TOMATO AGAMOUS-LIKE1 regulate different subsets of the known RIN targets, probably in a protein complex with the latter.

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“…To elucidate the biological processes that are involved in each gene expression cluster, overrepresentation analysis was performed using MetGenMAP (Joung et al, 2009). Pathways that are enriched among the overexpressed transcripts include many that are associated with plant defense and stress responses (Fig.…”

Section: Clustering Of Expression Patterns In the Transcriptome Datamentioning

confidence: 99%

Dynamic maize responses to aphid feeding are revealed by a time series of transcriptomic and metabolomic assays

et al. 2015

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(A.H.); 0000-0002-9675-934X (G.J.).As a response to insect attack, maize (Zea mays) has inducible defenses that involve large changes in gene expression and metabolism. Piercing/sucking insects such as corn leaf aphid (Rhopalosiphum maidis) cause direct damage by acquiring phloem nutrients as well as indirect damage through the transmission of plant viruses. To elucidate the metabolic processes and gene expression changes involved in maize responses to aphid attack, leaves of inbred line B73 were infested with corn leaf aphids for 2 to 96 h. Analysis of infested maize leaves showed two distinct response phases, with the most significant transcriptional and metabolic changes occurring in the first few hours after the initiation of aphid feeding. After 4 d, both gene expression and metabolite profiles of aphid-infested maize reverted to being more similar to those of control plants. Although there was a predominant effect of salicylic acid regulation, gene expression changes also indicated prolonged induction of oxylipins, although not necessarily jasmonic acid, in aphid-infested maize. The role of specific metabolic pathways was confirmed using Dissociator transposon insertions in maize inbred line W22. Mutations in three benzoxazinoid biosynthesis genes, Bx1, Bx2, and Bx6, increased aphid reproduction. In contrast, progeny production was greatly decreased by a transposon insertion in the single W22 homolog of the previously uncharacterized B73 terpene synthases TPS2 and TPS3. Together, these results show that maize leaves shift to implementation of physical and chemical defenses within hours after the initiation of aphid feeding and that the production of specific metabolites can have major effects in maize-aphid interactions.

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Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology

Cited by 148 publications

References 64 publications

Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening

Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening

The Tomato FRUITFULL Homologs TDR4/FUL1 and MBP7/FUL2 Regulate Ethylene-Independent Aspects of Fruit Ripening

Dynamic maize responses to aphid feeding are revealed by a time series of transcriptomic and metabolomic assays

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