# Evaluation of genetically engineered crops using transcriptomic, proteomic, and metabolomic profiling techniques.

Agnès E Ricroch, Jean B Bergé, Marcel Kuntz

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Agnès E Ricroch, Jean B Bergé, Marcel Kuntz. Evaluation of genetically engineered crops using transcriptomic, proteomic, and metabolomic profiling techniques. Plant Physiology, 2011, 155 (4), pp.1752-61. 10.1104/pp.111.173609. hal-00590803

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Submitted on 29 May 2020

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<table><caption>**Supplemental Table 3: Comparison of GE varieties with altered metabolic traits with non-GE varieties.**</caption><thead><tr><th>Species</th><th>Techniques: T, transcriptomics P, proteomics; M, metabolomics</th><th>References</th><th>Varieties or traits</th><th>Differences in GE with respect to control</th><th>Differences between non-GE lines, timepoints or link to environment</th></tr></thead><tbody><tr><td>Barley</td><td>T</td><td>Hansen et al. (2007)</td><td>C-Hordein anti-sense in Golden Promise background (greenhouse-grown plants)</td><td>In seeds, C-Hordein decreased and sulphur-rich Hordein increased, increasing the demand for sulphur and S-aminoacids resulting in an upregulation of key genes. In total 139 genes up or down regulated. Changes in amino acid content (up to 18% for cystein)</td><td></td></tr><tr><td>Grapevine</td><td>T</td><td>Cutanda-Perez et al. (2009)</td><td>Constitutive ectopic expression of VlmybA1-2 (regulatory gene) into hairy roots and plants. VvMYBA1 transcription factor controls the expression of UDP-glucose:flavonoid 3-O-glucosyltransferase</td><td>De novo production of anthocyanins in all transgenic vegetative organs. Activation of only few genes, most involved in both proanthocyanidin and anthocyanin biosynthesis.</td><td></td></tr><tr><td></td><td>P</td><td>Sauvage et al. (2007)</td><td>Modified levels of alcohol dehydrogenase activity. Control, sense, and antisense</td><td>Changes in carbon metabolism-associated proteins in leaves</td><td></td></tr></tbody></table>
<table><tr><td rowspan="4">Potato</td><td>T</td><td>Baroja-Fernández et al. (2009)</td><td>lines grown in greenhouse<br/>Sucrose synthase overexpressed and antisensed in tuber</td><td>Antisense line: 186 genes down-regulated and 171 genes upregulated.<br/>Overexpressing line: 60 genes down-regulated and 58 genes up-regulated</td></tr><tr><td>P</td><td>Lehesranta et al. (2005)</td><td>Range of diverse varieties, landraces and GE lines (empty vector or potato sense and antisense Mal1 gene or antisense S-adenosylmethionine decarboxylase (SamDC) gene</td><td>No new protein; differences in a total of 9 proteins out of 730</td></tr><tr><td>M</td><td>Defernez et al. (2004)</td><td>Same as Lehesranta et al. (2005), plus sense and antisense fructokinase gene (40 GE lines and controls)</td><td>GE with modified polyamine content: significant differences in proline, trigonelline and numerous phenolics. Certain other GE lines: several compounds in higher or lower amounts (no more than 2–3x)</td></tr><tr><td>M</td><td>Catchpole et al. (2005)</td><td>Expression of globe artichoke sucrose:sucrose 1-fructosyltransferase, or this gene together with 1-fructan:fructan 1-fructosyltransferase</td><td>Composition of GE within the natural metabolite range and very similar to the progenitor line, with the exception of the predictable up-regulation</td></tr></table>
<table><tr><td></td><td></td><td></td><td>of some fructans and their expected derivatives</td><td></td></tr><tr><td></td><td>M</td><td>Kim et al. (2009)</td><td>Constitutively expression of human beta amyloid, curdlan synthase or glycogen synthase</td><td>Neither quantitative nor qualitative differences found between GE and controls</td></tr><tr><td></td><td>Targeted compositional analysis</td><td>Shepherd et al. (2006)</td><td>Same as Defernez et al. (2004)</td><td>Some differences but not consistent in soluble carbohydrates, glycoalkaloids, vitamin C, total nitrogen and fatty acids</td></tr><tr><td>Rice</td><td>T</td><td>Dubouzet et al. (2007)</td><td>Feedback-insensitive alpha subunit of rice anthranilate synthase leading to high tryptophan content in seeds</td><td>In 8-day-old seedlings: higher levels of anthranilate, tryptamine, and serotonin; about 12 out of 21,500 genes showed significant differential expression</td></tr><tr><td></td><td>T</td><td>Beatty et al. (2009)</td><td>Over-expression of alanine aminotransferase to obtain a strong nitrogen use efficiency phenotype. Plants grown hydroponically</td><td>0.11% and 0.07% differentially regulated genes in roots and shoots</td></tr><tr><td></td><td>P</td><td>Islam et al. (2005)</td><td>Seed expression of a sunflower seed albumin gene</td><td>Lower amounts (21% to 68%) of 4 glutelin and 1 globulin in GE mature seeds. varied from, suggesting re-allocation of sulfur reserves from endogenous proteins to</td></tr></table>
<table><tr><td></td><td></td><td></td><td></td><td>the sulfur sink in transgenic grain</td><td></td></tr><tr><td></td><td>M</td><td>Wakasa et al. (2006)</td><td>Feedback-insensitive alpha subunit of rice anthranilate synthase leading to high tryptophan content in seeds</td><td>164-265x increase in free tryptophan, predicable 2x increase in the amount of indole acetic acid, increase in other free amino acids (up to 5.2x for alanine), no substantial change in the amount of other phenolic compounds</td><td></td></tr><tr><td></td><td>P,M</td><td>Takahashi et al. (2005)</td><td>Expression of YK1, a homolog of maize HC-toxin reductase, conferring tolerance to several stresses</td><td>Slight differences in metabolites content between control and YK1 callus, but nearly identical in leaf and panicle (greenhouse). Proteome of cultured cells: higher levels for 5 spots out of 668</td><td></td></tr><tr><td rowspan="2">Tomato</td><td>T, M</td><td>Enfissi et al. (2010)</td><td>Down-regulation of DE-ETIOLATED-1 to improve nutritional antioxidant content</td><td>Widespread effects on diverse sectors of metabolism</td><td></td></tr><tr><td>T, M</td><td>Matto and Handa 2007 (review)</td><td>Fruit-specific expression of a yeast S-adenosylmethionine decarboxylase gene leading to high spermidine and spermine levels</td><td>One-quarter of 1067 genes differentially regulated during fruit ripening. Multiple metabolic pathways influenced and prominently: levels of choline, Glu, Gln,</td><td></td></tr></table>
<table><tr><td></td><td></td><td></td><td></td><td>Asn, citrate, malate and fumarate increased ; Asp, Thr, Val, glucose and sucrose decreased.</td><td></td></tr><tr><td>M</td><td>Le Gall et al. (2003)</td><td>Maize transcription factors LC and C1 were simultaneously overexpressed with the aim of increasing amounts of flavonols in ripe fruit</td><td>Significantly increase for 6 main flavonoid glycosides, differences for at least 15 other metabolites including citric acid, sucrose, phenylalanine, and trigonelline</td><td>Changes in GE line were less than 3x and within the natural variation of field-grown crops</td></tr><tr><td>M</td><td>Long et al. (2006)<br/>See also Bino et al. (2005) for non-GE mutant hp-2dg</td><td>Carotenoid mutants: Og, rr, hp; GE over-expressing phytoene desaturase or 1-deoxyxylulose-5-phosphate synthase; Antisense ferulate 5-hydroxylase</td><td>Metabolic changes limited to modified pathways for GE lines</td><td>Several metabolisms altered (elevated chlorogenic acid, rutin and carotenoid content) in high-pigment (hp) mutant</td></tr><tr><td>M</td><td>Fraser et al. (2007)</td><td>Over-expression of a phytoene synthase gene increasing carotenoid content</td><td>Specific sectors of metabolism altered in green fruit, levels of 43% of the metabolites significantly altered in ripe fruit (elevation in amino acid and fatty acid content)</td><td></td></tr><tr><td>M</td><td>Giliberto et al. (2005)</td><td>GE lines up-regulating the cryptochrome-2 gene</td><td>Overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and</td><td></td></tr></table>
<table><tr><td rowspan="3">Wheat</td><td>T</td><td>Baudo et al. (2006, 2009)<br/>See also Shewry et al. (2007) for a review</td><td>GE and conventionally-bred lines expressing in endosperm a set of genes encoding subunits of glutenin. GE also express bar gene in leaves</td><td>lycopene in fruits<br/>Differently expressed genes between GE and parent in endosperm: 0.02-0.05% (depending on development stage), leaves: 0.06%.<br/>Differently expressed genes between GE and non-GE (with same set of glutenins) in endosperm: 1.6-1.3%, leaves: 0.04%.</td><td>Differently expressed genes between conventionally-bred lines in endosperm: 5,7-1%, leaves: 0.27%</td></tr><tr><td>M</td><td>Baker et al. (2006), Beale et al. (2009)<br/>See also Shewry et al. (2007) for a review</td><td>GE and conventionally-bred lines expressing in endosperm a set of genes encoding subunits of glutenin</td><td>Polar metabolites studied. Differences in aminoacid composition generally within the same range as the one between control lines grown on different sites and in different years</td><td>Stronger influence of site and year than of genotype</td></tr><tr><td>M</td><td>Stamova et al. (2009)</td><td>Dx5 glutenin subunit expressing lines (+ bar gene) compared to lines with bar gene alone.<br/>Developing grain studied in greenhouse</td><td>Most metabolic changes were transient during development. Only 3 metabolite changes validated (guanine, 4-hydroxycinnamic acid and unknown)</td><td></td></tr></table>

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