The missing link to elucidate plant secondary metabolism

combining transcriptional profiling with targeted metabolome analysis

Heiko Rischer, Suvi T. Häkkinen, Alain Goossens, Tuulikki Seppänen-Laakso, Into Laakso, Dirk Inze, Kirsi-Marja Oksman-Caldentey

Research output: Contribution to conferenceConference articleScientific

Abstract

Despite the fact that currently about 25% of all pharmaceuticals are plant derived, including high value compounds like paclitaxel for which chemical synthesis is economically unfeasible, there are only very few examples for commercial exploitation of cell cultures. This is due to the exceedingly empirical nature of selecting high yielding clones and their long-term production instability. The lack of knowledge to fully understand the complex biosynthetic pathways in the plants adds to the problem. In order to gain a full picture of the secondary metabolism in plants we have developed a unique technology which combines genomics and metabolomics. The potential of this method is demonstrated in the model system of tobacco BY-2 cell cultures. A cDNA-AFLP transcript profiling was combined with a targeted metabolome analysis in methyl jasmonate elicited cells. From the 20000 transcript tags visualised in total 591 were jasmonate-modulated. In silico analysis further revealed that half of these genes are of special interest because of their early induction. 18% display no homology to any known sequence, whereas 64 % are similar to genes with a known function and 18% are similar to genes without a known function. After the conversion of the gene tags into full-length cDNAs and their cloning into suitable vectors the functional analysis is performed by overexpression / co-suppression in transformed cell lines. Besides identifying several novel genes we were able to characterize poorly understood branches of secondary metabolite biosynthetic pathways in tobacco, leading for example to alkaloids, by using hyphenated analytical tools like GC- and HPLC-MS. The great advantage of the new technology platform is its universal application to any plant or plant cell culture of interest.
Original languageEnglish
Publication statusPublished - 2003
MoE publication typeNot Eligible
EventConference on Plant-Made Pharmaceuticals 2003 - Quebec, Canada
Duration: 16 Mar 200319 Mar 2003

Conference

ConferenceConference on Plant-Made Pharmaceuticals 2003
CountryCanada
CityQuebec
Period16/03/0319/03/03

Fingerprint

metabolomics
metabolism
cell culture
biochemical pathways
tobacco
genes
gene conversion
paclitaxel
methyl jasmonate
secondary metabolites
amplified fragment length polymorphism
molecular cloning
alkaloids
cell lines
clones
genomics
drugs
synthesis
cells

Cite this

Rischer, H., Häkkinen, S. T., Goossens, A., Seppänen-Laakso, T., Laakso, I., Inze, D., & Oksman-Caldentey, K-M. (2003). The missing link to elucidate plant secondary metabolism: combining transcriptional profiling with targeted metabolome analysis. Paper presented at Conference on Plant-Made Pharmaceuticals 2003, Quebec, Canada.
Rischer, Heiko ; Häkkinen, Suvi T. ; Goossens, Alain ; Seppänen-Laakso, Tuulikki ; Laakso, Into ; Inze, Dirk ; Oksman-Caldentey, Kirsi-Marja. / The missing link to elucidate plant secondary metabolism : combining transcriptional profiling with targeted metabolome analysis. Paper presented at Conference on Plant-Made Pharmaceuticals 2003, Quebec, Canada.
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title = "The missing link to elucidate plant secondary metabolism: combining transcriptional profiling with targeted metabolome analysis",
abstract = "Despite the fact that currently about 25{\%} of all pharmaceuticals are plant derived, including high value compounds like paclitaxel for which chemical synthesis is economically unfeasible, there are only very few examples for commercial exploitation of cell cultures. This is due to the exceedingly empirical nature of selecting high yielding clones and their long-term production instability. The lack of knowledge to fully understand the complex biosynthetic pathways in the plants adds to the problem. In order to gain a full picture of the secondary metabolism in plants we have developed a unique technology which combines genomics and metabolomics. The potential of this method is demonstrated in the model system of tobacco BY-2 cell cultures. A cDNA-AFLP transcript profiling was combined with a targeted metabolome analysis in methyl jasmonate elicited cells. From the 20000 transcript tags visualised in total 591 were jasmonate-modulated. In silico analysis further revealed that half of these genes are of special interest because of their early induction. 18{\%} display no homology to any known sequence, whereas 64 {\%} are similar to genes with a known function and 18{\%} are similar to genes without a known function. After the conversion of the gene tags into full-length cDNAs and their cloning into suitable vectors the functional analysis is performed by overexpression / co-suppression in transformed cell lines. Besides identifying several novel genes we were able to characterize poorly understood branches of secondary metabolite biosynthetic pathways in tobacco, leading for example to alkaloids, by using hyphenated analytical tools like GC- and HPLC-MS. The great advantage of the new technology platform is its universal application to any plant or plant cell culture of interest.",
author = "Heiko Rischer and H{\"a}kkinen, {Suvi T.} and Alain Goossens and Tuulikki Sepp{\"a}nen-Laakso and Into Laakso and Dirk Inze and Kirsi-Marja Oksman-Caldentey",
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note = "Conference on Plant-Made Pharmaceuticals 2003 ; Conference date: 16-03-2003 Through 19-03-2003",

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Rischer, H, Häkkinen, ST, Goossens, A, Seppänen-Laakso, T, Laakso, I, Inze, D & Oksman-Caldentey, K-M 2003, 'The missing link to elucidate plant secondary metabolism: combining transcriptional profiling with targeted metabolome analysis' Paper presented at Conference on Plant-Made Pharmaceuticals 2003, Quebec, Canada, 16/03/03 - 19/03/03, .

The missing link to elucidate plant secondary metabolism : combining transcriptional profiling with targeted metabolome analysis. / Rischer, Heiko; Häkkinen, Suvi T.; Goossens, Alain; Seppänen-Laakso, Tuulikki; Laakso, Into; Inze, Dirk; Oksman-Caldentey, Kirsi-Marja.

2003. Paper presented at Conference on Plant-Made Pharmaceuticals 2003, Quebec, Canada.

Research output: Contribution to conferenceConference articleScientific

TY - CONF

T1 - The missing link to elucidate plant secondary metabolism

T2 - combining transcriptional profiling with targeted metabolome analysis

AU - Rischer, Heiko

AU - Häkkinen, Suvi T.

AU - Goossens, Alain

AU - Seppänen-Laakso, Tuulikki

AU - Laakso, Into

AU - Inze, Dirk

AU - Oksman-Caldentey, Kirsi-Marja

PY - 2003

Y1 - 2003

N2 - Despite the fact that currently about 25% of all pharmaceuticals are plant derived, including high value compounds like paclitaxel for which chemical synthesis is economically unfeasible, there are only very few examples for commercial exploitation of cell cultures. This is due to the exceedingly empirical nature of selecting high yielding clones and their long-term production instability. The lack of knowledge to fully understand the complex biosynthetic pathways in the plants adds to the problem. In order to gain a full picture of the secondary metabolism in plants we have developed a unique technology which combines genomics and metabolomics. The potential of this method is demonstrated in the model system of tobacco BY-2 cell cultures. A cDNA-AFLP transcript profiling was combined with a targeted metabolome analysis in methyl jasmonate elicited cells. From the 20000 transcript tags visualised in total 591 were jasmonate-modulated. In silico analysis further revealed that half of these genes are of special interest because of their early induction. 18% display no homology to any known sequence, whereas 64 % are similar to genes with a known function and 18% are similar to genes without a known function. After the conversion of the gene tags into full-length cDNAs and their cloning into suitable vectors the functional analysis is performed by overexpression / co-suppression in transformed cell lines. Besides identifying several novel genes we were able to characterize poorly understood branches of secondary metabolite biosynthetic pathways in tobacco, leading for example to alkaloids, by using hyphenated analytical tools like GC- and HPLC-MS. The great advantage of the new technology platform is its universal application to any plant or plant cell culture of interest.

AB - Despite the fact that currently about 25% of all pharmaceuticals are plant derived, including high value compounds like paclitaxel for which chemical synthesis is economically unfeasible, there are only very few examples for commercial exploitation of cell cultures. This is due to the exceedingly empirical nature of selecting high yielding clones and their long-term production instability. The lack of knowledge to fully understand the complex biosynthetic pathways in the plants adds to the problem. In order to gain a full picture of the secondary metabolism in plants we have developed a unique technology which combines genomics and metabolomics. The potential of this method is demonstrated in the model system of tobacco BY-2 cell cultures. A cDNA-AFLP transcript profiling was combined with a targeted metabolome analysis in methyl jasmonate elicited cells. From the 20000 transcript tags visualised in total 591 were jasmonate-modulated. In silico analysis further revealed that half of these genes are of special interest because of their early induction. 18% display no homology to any known sequence, whereas 64 % are similar to genes with a known function and 18% are similar to genes without a known function. After the conversion of the gene tags into full-length cDNAs and their cloning into suitable vectors the functional analysis is performed by overexpression / co-suppression in transformed cell lines. Besides identifying several novel genes we were able to characterize poorly understood branches of secondary metabolite biosynthetic pathways in tobacco, leading for example to alkaloids, by using hyphenated analytical tools like GC- and HPLC-MS. The great advantage of the new technology platform is its universal application to any plant or plant cell culture of interest.

M3 - Conference article

ER -

Rischer H, Häkkinen ST, Goossens A, Seppänen-Laakso T, Laakso I, Inze D et al. The missing link to elucidate plant secondary metabolism: combining transcriptional profiling with targeted metabolome analysis. 2003. Paper presented at Conference on Plant-Made Pharmaceuticals 2003, Quebec, Canada.