A functional genomics approach to unravel plant secondary metabolism by combining transcriptional profiling with targeted metabolome analysis

Research output: Contribution to conferenceConference articleScientific

Abstract

Plant cell cultures are an option for producing secondary metabolites useful for diverse applications although only very few economically feasible examples exist so far. Engineering of plant cells with functionally tested genes helps to understand the biosynthetic pathways and is the method of choice for creating high yielding strains for commercial production. On a genome wide scale genes involved in plant secondary metabolism are simultaneously identified and isolated by an approach, in which a cDNA-AFLP based transcript profiling technique in conjunction with metabolic pathway profiling is applied. Highly specific RNA fingerprints in function of time are obtained following elicitation of cell cultures. In parallel the quantitative and qualitative changes of metabolites involved in selected pathways are determined by several hyphenated methods (e.g. GC-MS, HPLC-MS). The functional testing of promising genes obtained from full-length cloning is done by analyzing the metabolic changes in overexpression/co-suppression experiments of transformed cells. A well-defined correlation between the pathway specific metabolites and the transcriptome was revealed using the model system of tobacco BY-2 cells. In silico analysis of about 20000 visualised gene tags showed that about 600 were differentially regulated by the elicitor. The applied analytical methods were sensitive enough for the investigated secondary compounds but the need for different extraction processes in order to analyze metabolites from different biosynthetic branches became obvious from comparing extraction efficiencies. First experiments with other plant species confirmed that the technology is principally applicable to any plant or plant cell culture of interest.
Original languageEnglish
Publication statusPublished - 2003
MoE publication typeNot Eligible
Event2nd International Conference Plant Metabolomics - Potsdam, Germany
Duration: 25 Apr 200328 Apr 2003

Conference

Conference2nd International Conference Plant Metabolomics
CountryGermany
CityPotsdam
Period25/04/0328/04/03

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metabolomics
genomics
metabolism
cell culture
metabolites
biochemical pathways
genes
cells
transcriptome
secondary metabolites
amplified fragment length polymorphism
analytical methods
molecular cloning
engineering
tobacco
high performance liquid chromatography
methodology
RNA
genome
testing

Cite this

@conference{35e8d576de18436390a72d02b3d3f7b0,
title = "A functional genomics approach to unravel plant secondary metabolism by combining transcriptional profiling with targeted metabolome analysis",
abstract = "Plant cell cultures are an option for producing secondary metabolites useful for diverse applications although only very few economically feasible examples exist so far. Engineering of plant cells with functionally tested genes helps to understand the biosynthetic pathways and is the method of choice for creating high yielding strains for commercial production. On a genome wide scale genes involved in plant secondary metabolism are simultaneously identified and isolated by an approach, in which a cDNA-AFLP based transcript profiling technique in conjunction with metabolic pathway profiling is applied. Highly specific RNA fingerprints in function of time are obtained following elicitation of cell cultures. In parallel the quantitative and qualitative changes of metabolites involved in selected pathways are determined by several hyphenated methods (e.g. GC-MS, HPLC-MS). The functional testing of promising genes obtained from full-length cloning is done by analyzing the metabolic changes in overexpression/co-suppression experiments of transformed cells. A well-defined correlation between the pathway specific metabolites and the transcriptome was revealed using the model system of tobacco BY-2 cells. In silico analysis of about 20000 visualised gene tags showed that about 600 were differentially regulated by the elicitor. The applied analytical methods were sensitive enough for the investigated secondary compounds but the need for different extraction processes in order to analyze metabolites from different biosynthetic branches became obvious from comparing extraction efficiencies. First experiments with other plant species confirmed that the technology is principally applicable 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",
year = "2003",
language = "English",
note = "2nd International Conference Plant Metabolomics ; Conference date: 25-04-2003 Through 28-04-2003",

}

Rischer, H, Häkkinen, ST, Goossens, A, Seppänen-Laakso, T, Laakso, I, Inze, D & Oksman-Caldentey, K-M 2003, 'A functional genomics approach to unravel plant secondary metabolism by combining transcriptional profiling with targeted metabolome analysis' Paper presented at 2nd International Conference Plant Metabolomics, Potsdam, Germany, 25/04/03 - 28/04/03, .

A functional genomics approach to unravel plant secondary metabolism by 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 2nd International Conference Plant Metabolomics, Potsdam, Germany.

Research output: Contribution to conferenceConference articleScientific

TY - CONF

T1 - A functional genomics approach to unravel plant secondary metabolism by 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 - Plant cell cultures are an option for producing secondary metabolites useful for diverse applications although only very few economically feasible examples exist so far. Engineering of plant cells with functionally tested genes helps to understand the biosynthetic pathways and is the method of choice for creating high yielding strains for commercial production. On a genome wide scale genes involved in plant secondary metabolism are simultaneously identified and isolated by an approach, in which a cDNA-AFLP based transcript profiling technique in conjunction with metabolic pathway profiling is applied. Highly specific RNA fingerprints in function of time are obtained following elicitation of cell cultures. In parallel the quantitative and qualitative changes of metabolites involved in selected pathways are determined by several hyphenated methods (e.g. GC-MS, HPLC-MS). The functional testing of promising genes obtained from full-length cloning is done by analyzing the metabolic changes in overexpression/co-suppression experiments of transformed cells. A well-defined correlation between the pathway specific metabolites and the transcriptome was revealed using the model system of tobacco BY-2 cells. In silico analysis of about 20000 visualised gene tags showed that about 600 were differentially regulated by the elicitor. The applied analytical methods were sensitive enough for the investigated secondary compounds but the need for different extraction processes in order to analyze metabolites from different biosynthetic branches became obvious from comparing extraction efficiencies. First experiments with other plant species confirmed that the technology is principally applicable to any plant or plant cell culture of interest.

AB - Plant cell cultures are an option for producing secondary metabolites useful for diverse applications although only very few economically feasible examples exist so far. Engineering of plant cells with functionally tested genes helps to understand the biosynthetic pathways and is the method of choice for creating high yielding strains for commercial production. On a genome wide scale genes involved in plant secondary metabolism are simultaneously identified and isolated by an approach, in which a cDNA-AFLP based transcript profiling technique in conjunction with metabolic pathway profiling is applied. Highly specific RNA fingerprints in function of time are obtained following elicitation of cell cultures. In parallel the quantitative and qualitative changes of metabolites involved in selected pathways are determined by several hyphenated methods (e.g. GC-MS, HPLC-MS). The functional testing of promising genes obtained from full-length cloning is done by analyzing the metabolic changes in overexpression/co-suppression experiments of transformed cells. A well-defined correlation between the pathway specific metabolites and the transcriptome was revealed using the model system of tobacco BY-2 cells. In silico analysis of about 20000 visualised gene tags showed that about 600 were differentially regulated by the elicitor. The applied analytical methods were sensitive enough for the investigated secondary compounds but the need for different extraction processes in order to analyze metabolites from different biosynthetic branches became obvious from comparing extraction efficiencies. First experiments with other plant species confirmed that the technology is principally applicable 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. A functional genomics approach to unravel plant secondary metabolism by combining transcriptional profiling with targeted metabolome analysis. 2003. Paper presented at 2nd International Conference Plant Metabolomics, Potsdam, Germany.