New Biotechnology  Volume 25S  September 2009 ABSTRACTS
3. PLANT & ENVIRONMENTAL
BIOTECHNOLOGY
3.5. OMICS
Oral
Systems response to environmental conditions as studied
by metabolome analysis
L. Willmitzer
, T. Degenkolbe, C. Caldana, M. Hannah
Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Ger-
many
The metabolome comprises the entity of small molecules present
in a given biological system. Due to its vast chemical diversity
resulting in major differences concerning extraction, purification
or detection, the development of metabolomics has lagged behind
the development of tools for genome-wide analysis on the RNA or
protein level.
A number of years ago we have started to develop mass
spectrometry based methods aiming at the high-throughput characterization
of the metabolome.
In the presentation examples will be discussed showing the
application of metabolomics in systems biology.
More specifically the kinetic response of A. thaliana towards
changing environmental conditions will be presented.
Correlation matrices will be evaluated using a variety of graph
tools and resulting hypothesis concerning the importance of certain
metabolites and pathways with respect to adjustment of the
biological system will be discussed.
doi:10.1016/j.nbt.2009.06.868
Plant metabolomics: a basis for plant functional
genomics and biotechnology
K. Saito
RIKEN Plant Science Center, Graduate School of Pharmaceutical Sciences, Chiba
University, Japan
Metabolomics, which deals with all metabolites of an organism, is
one of the major components of omics research. It plays significant
roles in a variety of fields from medicines to agriculture and holds
a fundamental position in functional genomics and biotechnology.
Metabolomics research is particularly important in the plant
field, because plants collectively produce a huge variety of chemical
compounds, far more than animals and even microorganisms.
In addition, most of the human-beneficial properties of plants
-- foods, medicinal resources, or industrial raw materials -- are
ascribed to plant metabolites.
Using Arabidopsis thaliana, an integrated analysis of
metabolome and transcriptome led to prediction of gene-tometabolite
relations. Co-regulation framework models of genes
and metabolites in the pathways of flavonoids, sulfur compounds
and lipids, suggested the specific involvement of co-expressed
genes in the synthesis and accumulation of the metabolites in the
pathways. Reverse genetic and reverse biochemistry confirmed
those delimited genes' functions in the pathways.
This strategy was further applicable to decipher the genes'
functions of medicinal plants rich with a variety of phytochemicals,
such as Perilla frutescens producing anthocyanins, Ophiorrhiza
pumila root cultures producing an anti-cancer alkaloid camptothecin
and Glycyrrhiza uralensis (licorice) producing natural
sweetener glycyrrhizin. These results suggest the versatility of integration
of metabolomics and transcriptomics for decoding the
genome basis underlying secondary metabolism.
For biotechnology application of metabolomics, the substantial
equivalence of GMO has been evaluated by a platform comprising
multiple mass spectrometers established in RIKEN. Metabolomics
1871-6784/$ -- see front matter www.elsevier.com/locate/nbt S317
ABSTRACTS New Biotechnology  Volume 25S  September 2009
on rice genetic resources led to the prediction of agronomical and
food traits of rice by regression analysis.
In this presentation, the crucial roles of metabolomics in plant
functional genomics and biotechnology will be discussed.
doi:10.1016/j.nbt.2009.06.869
Functional proteomics: a cornerstone in plant systems
biology
S. Bischof
, S. Reiland, K. Baerenfaller, A.P. Barba de la Rosa, P.
Schläpfer, R. Trösch, W. Gruissem, S. Baginsky
Institute of Plant Sciences, Swiss Federal Institute of Technology, 8092 Zurich,
Switzerland
We have assembled a proteome map for Arabidopsis thaliana
from high-density, organ-specific proteome catalogs. We matched
95,988 unique peptides to 14,179 proteins and provide expression
evidence for a number of gene models that are not represented
in the TAIR8 protein database. Analysis of the proteome identified
organ-specific biomarkers and allowed us to compile an
organ-specific set of proteotypic peptides for 4105 proteins to
facilitate targeted quantitative proteomics surveys. On the basis
of proteome maps for cell organelles, we compared the quantitative
proteome composition of different cell organelles in the
different organs, and generated flux-balance models of plastid
metabolism in seeds, roots and leaves. Current organellar proteome
maps are not exhaustive, and we therefore analyzed the
proteome of two plastid protein import mutants, ppi1 and ppi2,
lacking components of the plastid protein import machinery.
These plastids are depleted of abundant photosynthetic proteins
and therefore provide an improved dynamic range for the characterization
of low abundance proteins. More than 1500 different
proteins were identified and quantified from isolated plastids.
Overall, the protein accumulation in the different mutants was
surprisingly similar suggesting basic robustness principles and limited
plasticity for the assembly of organellar proteomes. In order
to further characterize chloroplast protein import in the different
mutants, we systematically searched for N-terminal acetylated
peptides in genome-scale WT, ppi1 and ppi2 proteomics data.
These analyses revealed the accumulation of precursor proteins
in the TOC159-deficient mutants (ppi2), probably as a result of
the impaired import reaction. We discuss these observations in
the context of protein import specificity and signaling pathways
for retrograde communication. In order to expand our grasp on
the dynamic regulation of the chloroplast proteome, we analyzed
the chloroplast phosphoproteome and its dynamics during a circadian
cycle. Motif-X analysis of the phosphorylation sites in
chloroplast proteins identified three significantly enriched kinase
motifs, which include known casein kinase II and proline-directed
kinase motifs. To identify the kinases responsible for the regulation
of chloroplast phosphoproteome dynamics, we characterized
the phosphoproteome of T-DNA insertion mutants for different
chloroplast kinases in comparison to wildtype in order to establish
their in vivo substrate spectrum. We present here our data obtained
with the thylakoid associated kinase STN8.
doi:10.1016/j.nbt.2009.06.870
Gene regulatory networks and transcription factor tran-
scriptomics
B. Mueller-Roeber1,2,
, S. Arvidsson1,2
, S. Balazadeh1,2
, L.G.G.
Corra1,2
, P. Pérez-Rodríguez1,3
, D.M. Ria~no-Pachón1,2
1
University of Potsdam, Department of Molecular Biology, Potsdam, Germany
2
Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
3
Colegio de Postgraduados, Campus Montecillo, Texcoco, México, Mexico
Transcription factors (TFs) are regulatory proteins that turn on
and off the activity of the genes they control (target genes), by
binding to short DNA elements (cis-regulatory elements; CREs)
in their promoter sequences, constituting important components
of gene regulatory networks (GRNs). TFs play important roles
in almost all biological processes and thus it is perhaps not
surprising that a large percentage of the genome encodes for
these regulatory proteins. Our lab studies the function of TFs
that control GRNs during development and biomass accumulation
of photosynthetic organisms, including higher plants and
photosynthetic micro-algae. Due to rapid progress in sequencing
technologies, more and more genome sequences are rapidly
becoming assessable providing an excellent resource for the analysis
the evolutionary and functional relationships of transcriptional
regulators across species. To speed up the discovery of TF genes we
have established a bio-computational pipeline and established the
Plant Transcription Factor Database (http://www.plntfdb.bio.unipotsdam.de),
which includes TF genes from micro-algae to higher
plants. At the experimental level we use multi-parallel quantitative
real-time polymerase chain reaction (qRT-PCR) to identify
TFs that are functionally important for leaf development, control
responses to changes in light and nutrient availability in the
alga Chlamydomonas reinhardtii, and affect abiotic stress tolerance
in rice and Arabidopsis. The available qRT-PCR platforms allow
the facile expression analyses of 2.000 TF genes in both rice
and Arabidopsis, and the known set of 240 transcriptional regulatory
genes in Chlamydomonas. To assist the development of
further qPCR platforms, we have established QuantPrime, a userfriendly,
fully automated tool for primer pair design (available
at www.quantprime.de). qRT-PCR has been demonstrated to be
superior to micro-array-based technologies in expression analyses
(providing higher sensitivity), enabling us to discover TF transcriptome
responses that remained undetected before. We are currently
developing a new experimental pipeline to support the discovery
of TF--TF control cascades in plants. Examples will be presented.
doi:10.1016/j.nbt.2009.06.871
S318 www.elsevier.com/locate/nbt