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Indian GM concerns
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TRENDS in Plant Science Vol.6 No.5 May 2001
191
Profiling modified metabolomes As the focus of post-genomic research shifts towards the elucidation of gene function, high throughput multi-parallel techniques have been developed for the analysis of both gene expression and the protein complement of a system. The latest addition to the repertoire of functional genomics is metabolic profiling, which enables the nonbiased, simultaneous determination of metabolite levels in whole-plant systems, thereby offering a direct link between a change in mRNA or protein and downstream factors that influence biological function. An approach pioneered by researchers in Germany, capable of the quantitative and qualitative detection of >300 compounds, was recently shown to enable the assignment of distinct metabolic profiles to different Arabidopsis thaliana genotypes. Ute Roessner et al.1 have now turned their attention towards determining the suitability of this approach for profiling metabolic changes in genetically and environmentally modified plants. To test the sensitivity of the technique, the authors chose a variety of transgenic potato lines that are all modified at the same metabolic locus: sucrose catabolism. Extracts of tubers expressing a yeast invertase (INV), a bacterial sucrose phosphorylase (SP), or both a bacterial glucokinase and yeast invertase (GK3) were fractionated, derivatized and analyzed by gas chromatography–mass spectrometry. The
levels of most of the 88 metabolites detected were altered compared with the wild type. Moreover, nine additional metabolites, including sugars, amino acids and organic acids, were detected in the transgenics and were mostly associated with specific genetic modifications. Maltose and trehalose, for example, were found only in GK3 and INV lines, whereas homoglutamine, homocysteine and a large unknown peak were only detected in SP lines. Applying ‘…breadth and unbiased nature [of metabolic profiling] highlights the potential for identifying unexpected changes in metabolism and unknown compounds.’ hierarchical cluster and principal component analyses to the data revealed that individual transformants grouped according to the genetic modification. Thus, wild-type and SP samples formed distinct clusters, whereas the GK3 lines were more closely associated with their parental line, INV-30. Therefore, even though sucrose phosphorylase and invertase act on the same molecule, the transgenic lines exhibited distinct metabolic profiles. Furthermore, the authors could ascertain the most important metabolic component(s) of each phenotype. The technique was equally sensitive to environmentally induced metabolic changes. Significant differences were detected between wild-type tuber discs incubated in 0–500 mM glucose, with the distance of
clusters from the wild-type steady state reflecting increasing glucose concentration. Glucose-fed tubers clustered closer to the wild-type steady state than to any of the transgenics. By phenotyping closely related genetically and environmentally modified plants, this study demonstrates the resolving power of a technique that is still in its infancy. The method offers a direct link between a given manipulation and the function of the metabolic network, and its breadth and unbiased nature highlights the potential for identifying unexpected changes in metabolism and unknown compounds. In conjunction with transgenic technology in particular, the technique should provide new insight into the regulation and relationships of plant metabolites and, through the elucidation of the chemical nature of unknown metabolites, it should help to identify new targets for gene discovery. As the list of detectable compounds grows, the comprehensive metabolic analysis of genetically modified crop plants might also serve to allay public fears over safety. 1 Roessner, U. et al. (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13, 11–29
Nicola T. Wood [email protected]
In Brief
A scents approach to genetic engineering Intensive cultivation of plants usually leads to the emphasis of some desirable characteristics at the expense of others; for example, flowers bred for showy blooms tend to lose much of their scent. In recognition of this, research at the Hebrew University of Jerusalem (Israel), which aims to create a DNA database of the genes responsible for flower scent, should soon be getting up everyone’s nose. Ultimately, the information should lead to an understanding of the biochemistry of flower perfume, and perhaps help to replace some of the lost bouquet. [Nature (2001) 410, 7] NC
Indian GM concerns Although growing GM plants is vociferously condemned in parts of the so-called developed world, it is widely believed that the developing world wants to use such crops. However, this perception is not necessarily correct. In India, for instance, plans to engineer and plant GM rice and mustard that make β-carotene (a precursor of vitamin A) are being greeted with resistance by ecologists and farmers’ organizations. Even though vitamin A deficiency is contributing to child mortality and causing blindness in children, there are concerns that GM technology is insufficiently tested and might not only be hazardous, but also inefficient. [Br. Med. J. (2001) 322, 126] NC
Arabidopsis, the new wonder crop? Now that the elation surrounding the recent completion of the sequencing of the Arabidopsis genome is dying down, plant scientists are faced with the problem of what to do with all the information. Unfortunately, claims that knowledge from this ephemeral weed will benefit work with crop plants have been greeted with some scepticism. However, Simcha Lev-Yadun of the University of Haifa (Israel) [Nat. Biotechnol. (2001) 19, 95] has ingeniously turned this argument around by suggesting that Arabidopsis itself should be developed as a crop plant. Perhaps we will be eating Arabidopsis quiche after all? NC
http://plants.trends.com 1360-1385/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved.
TRENDS in Plant Science Vol.6 No.5 May 2001
191
Profiling modified metabolomes As the focus of post-genomic research shifts towards the elucidation of gene function, high throughput multi-parallel techniques have been developed for the analysis of both gene expression and the protein complement of a system. The latest addition to the repertoire of functional genomics is metabolic profiling, which enables the nonbiased, simultaneous determination of metabolite levels in whole-plant systems, thereby offering a direct link between a change in mRNA or protein and downstream factors that influence biological function. An approach pioneered by researchers in Germany, capable of the quantitative and qualitative detection of >300 compounds, was recently shown to enable the assignment of distinct metabolic profiles to different Arabidopsis thaliana genotypes. Ute Roessner et al.1 have now turned their attention towards determining the suitability of this approach for profiling metabolic changes in genetically and environmentally modified plants. To test the sensitivity of the technique, the authors chose a variety of transgenic potato lines that are all modified at the same metabolic locus: sucrose catabolism. Extracts of tubers expressing a yeast invertase (INV), a bacterial sucrose phosphorylase (SP), or both a bacterial glucokinase and yeast invertase (GK3) were fractionated, derivatized and analyzed by gas chromatography–mass spectrometry. The
levels of most of the 88 metabolites detected were altered compared with the wild type. Moreover, nine additional metabolites, including sugars, amino acids and organic acids, were detected in the transgenics and were mostly associated with specific genetic modifications. Maltose and trehalose, for example, were found only in GK3 and INV lines, whereas homoglutamine, homocysteine and a large unknown peak were only detected in SP lines. Applying ‘…breadth and unbiased nature [of metabolic profiling] highlights the potential for identifying unexpected changes in metabolism and unknown compounds.’ hierarchical cluster and principal component analyses to the data revealed that individual transformants grouped according to the genetic modification. Thus, wild-type and SP samples formed distinct clusters, whereas the GK3 lines were more closely associated with their parental line, INV-30. Therefore, even though sucrose phosphorylase and invertase act on the same molecule, the transgenic lines exhibited distinct metabolic profiles. Furthermore, the authors could ascertain the most important metabolic component(s) of each phenotype. The technique was equally sensitive to environmentally induced metabolic changes. Significant differences were detected between wild-type tuber discs incubated in 0–500 mM glucose, with the distance of
clusters from the wild-type steady state reflecting increasing glucose concentration. Glucose-fed tubers clustered closer to the wild-type steady state than to any of the transgenics. By phenotyping closely related genetically and environmentally modified plants, this study demonstrates the resolving power of a technique that is still in its infancy. The method offers a direct link between a given manipulation and the function of the metabolic network, and its breadth and unbiased nature highlights the potential for identifying unexpected changes in metabolism and unknown compounds. In conjunction with transgenic technology in particular, the technique should provide new insight into the regulation and relationships of plant metabolites and, through the elucidation of the chemical nature of unknown metabolites, it should help to identify new targets for gene discovery. As the list of detectable compounds grows, the comprehensive metabolic analysis of genetically modified crop plants might also serve to allay public fears over safety. 1 Roessner, U. et al. (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13, 11–29
Nicola T. Wood [email protected]
In Brief
A scents approach to genetic engineering Intensive cultivation of plants usually leads to the emphasis of some desirable characteristics at the expense of others; for example, flowers bred for showy blooms tend to lose much of their scent. In recognition of this, research at the Hebrew University of Jerusalem (Israel), which aims to create a DNA database of the genes responsible for flower scent, should soon be getting up everyone’s nose. Ultimately, the information should lead to an understanding of the biochemistry of flower perfume, and perhaps help to replace some of the lost bouquet. [Nature (2001) 410, 7] NC
Indian GM concerns Although growing GM plants is vociferously condemned in parts of the so-called developed world, it is widely believed that the developing world wants to use such crops. However, this perception is not necessarily correct. In India, for instance, plans to engineer and plant GM rice and mustard that make β-carotene (a precursor of vitamin A) are being greeted with resistance by ecologists and farmers’ organizations. Even though vitamin A deficiency is contributing to child mortality and causing blindness in children, there are concerns that GM technology is insufficiently tested and might not only be hazardous, but also inefficient. [Br. Med. J. (2001) 322, 126] NC
Arabidopsis, the new wonder crop? Now that the elation surrounding the recent completion of the sequencing of the Arabidopsis genome is dying down, plant scientists are faced with the problem of what to do with all the information. Unfortunately, claims that knowledge from this ephemeral weed will benefit work with crop plants have been greeted with some scepticism. However, Simcha Lev-Yadun of the University of Haifa (Israel) [Nat. Biotechnol. (2001) 19, 95] has ingeniously turned this argument around by suggesting that Arabidopsis itself should be developed as a crop plant. Perhaps we will be eating Arabidopsis quiche after all? NC
http://plants.trends.com 1360-1385/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved.