for an





Integrated Project






The Yeast Silicon Cell: a molecular systems biology approach

Acronym: YSiC

Prepared by

Università degli Studi di Milano-Bicocca, Milan, Italy

BioCentrum Amsterdam, The Netherlands

Göteborg University, Göteborg, Sweden

Katholieke Universiteit Leuven, Leuven, Belgium

Oxford Brookes University, Oxford, United Kingdom

University of Stuttgart, Stuttgart, Germany





This Expression of Interest was submitted in response to Call EOI.FP6.2002

4th June 2002

Coordinator: Prof. Lilia Alberghina

Dept. of Biotechnology and Bioscience

University of Milan-Bicocca

P.zza della Scienza, 2 - Milano, Italy


Co-coordinator: Prof. Hans V. Westerhoff

Molecular Cell Physiology

Faculty of Earth and Life Sciences

Free University, De Boelelaan 1087

NL-1081 HV Amsterdam, The Netherlands



1. Aim of the proposed work

The goal of this proposal for an Integrated Project is to concentrate experimental and computational efforts toward the development of a Yeast Silicon Cell (YSiC) i.e. the first computer replica of an eukaryotic model organism, the unicellular budding yeast Saccharomyces cerevisiae. The deliverables will be progressively refined models, suitable to be tailored to specific research and industrial needs. The achievement of this goal will be of tremendous importance for:


1.1 Contribution to Priority Thematic Area of Framework 6

The research priority sub-theme 1.1.1.ia addresses the development of fundamental knowledge and basic tools for functional genomics in all organisms. In particular the topic "Multidisciplinary functional genomics approaches to basic biological processes" that will focus on the elucidation of the mechanisms underlying fundamental cellular processes and that stresses the importance of integrating multiple disciplines (genomics, proteomics, bioinformatics) appears to give a very appropriate frame to the present YSiC IP. The broader research priority 1.1.1. of Genomics and Biotechnology for Human Health will be served with the development of the proposed part of the first silicon yeast cell (the main deliverable of this IP). Even a partial replica of the yeast cell can be used to dry-test new drugs, new dosages and new combinations of existing drugs. In particular drugs that are meant to affect cell cycling can be accommodated. Although yeast is obviously not identical to mammalian cells, it is already now widely used by pharmaceutical companies for drug discovery and testing. Because of the low cost, initial testing of drugs in a YSiC will be of great interest to pharmaceutical companies.


1.2 Contribution to the European Research Area

The proposed work will serve to structure and integrate EU research by coordinating research efforts and addressing the issue of underfinanced research. An Integrated Project may be better suited than a Network of Excellence to the delivery of a product, the YSiC, that can be achieved only through a concerted and highly focused scientific and technological effort. This IP will be part of the large European Systems Biology Supranetwork ESBIGH []. It is also planned a strong connection with a NoE coordinated by Johan Thevelein, leader of one of the core groups of this IP, focusing on Yeast Signal Transduction and eventually with other pertinent NoEs.



2. Background to the Proposed IP

The information delivered by genome sequencing, transcriptome, metabolome and proteome analyses - including protein/protein and protein/nucleic acid interaction maps -, is so extensive and complex that it runs the danger of undergoing the same fate as much of the scientific information gathered in the last century: to be accumulated but never applied. In addition to serving as an ordering force for all the molecular information, the silicon organism that will be produced will have a number of important uses. It will greatly foster our understanding of the real organism by allowing in silico experiments aimed at understanding and predicting the complex phenotypes resulting from the interaction of many gene products and by the molecules interacting with them. In addition the definition of a molecular blueprint that describes the various cellular events and their control should structure new experiments and allow quantitative predictive ability.

Computer implementations of some cellular processes, such as signal transduction and metabolic pathways have already been described. The so called in silico cell goes several steps further along this line by integrating each relevant model within a common framework aimed to replicate in silico the major properties of the life cycle of the chosen model cell, i.e. energy transduction, cell mass growth, DNA replication and cell division.

S. cerevisiae has played a pioneering role in eukaryotic cell biology. It continues to serve as a model and tool to unravelling the molecular basis of a wide variety of cellular phenomena also in mammalian cells, given the fact that the more important cellular processes such as metabolism, signal transduction, bioenergetics, control of gene-expression, cell cycle, ageing, apoptosis are conserved from yeast to man. For these reasons and because the tools available today in yeast are years ahead of those available for other organisms, budding yeast has been and will continue to be highly relevant also to investigate at the cellular level human functions for drug discovery purposes and for clinical applications. Budding yeast is also the only model organism having its own relevant biotechnological role, for instance in the food and chemical industry and as an host serving for expression of heterologous proteins of biotechnological interest. These combined elements make S. cerevisiae the best choice to be the first eukaryotic model organism with which to attempt to construct a silicon cell. S. cerevisiae carbon metabolism has already been modelled and is available for in silico experimentation (see the web site of this consortium: Cell cycle events have also been modelled by a systems biology approach; molecular determinants and regulatory circuits of the cell sizer controlling the entrance into S phase have been identified. Furthermore quantitative relations between metabolism and cell cycle parameters have been ascertained. Taken together these results indicate that it is now possible to develop a blueprint describing at least the more relevant events of signal transduction, carbon metabolism, growth and cell cycle in a relatively short period of time (3-5 years) given the appropriate human, technological and financial resources.


3. Expected Results from the Proposed IP

The making of an in silico replica of an entire cell, or even a significant part of it, is impossible for a single scientific group, as the diversity of the expertise required is much too broad. The aim of this project is thus to gather the best European groups working on several key aspects of yeast cell physiology in order to develop in silico replicas of recognizable parts of the yeast cell (modules) and then to connect these to each other. Therewith the YSiC IP will increase EU competitiveness in the area of drug discovery and fermentation technology by making available the following deliverables:

Users of the delivered YSiC(s) in either basic or specifically tailored versions will include academic research institutions as well as industrial research and development departments, notably from high-tech SMEs.


4. Activities to Achieve the Proposed Objectives

In the development of new concepts for a YSiC, the consortium intends to integrate the two main streams of systems biology (Figure 1). A bottom-up approach attempts to aggregate biological knowledge at the molecular level including the quantitative description of their dynamic interactions (kinetics). This leads to modules, i.e discrete entities whose functions are quasi-autonomous, that function in silico. The higher level properties – the behavior of cells – will be described by connecting these in silico modules. A complementary, top-down strategy is based on a system oriented decomposition that also makes use of genome-wide experimental data. By means of this reverse engineering approach, molecular knowledge is extracted from the global systems behavior.

Figure 1 Alternative approaches to systems biology

A scheme of the integration of activities of the IP is reported in Figure 2 below.

5. Information for interested partners

So far only a few national Systems Biology programs (USA, Japan, Germany, and Canada) and only one explicit Silicon Cell program ( have been launched. Only the focus of the FP6 on strong interdisciplinary and trans-national research can nucleate the required European integration bringing together the needed scientific and technological excellence and critical mass. This will enhance European scientific and technological excellence in this emerging new discipline where Europe can be leader. The European dimension will allow the tightly-knit cooperation of many groups working on specific subsystems, allowing the coordinated generation of the specific quantitative data needed to implement the model of the specified components. To this end different type of units will be organised. Computing Units (CU, data mining, modelling, computer implementation); Data Collection Units (DCU, molecular physiology, biochemistry, molecular biology, genome-wide techniques); Database management and visualisation Units (DBU, to display the network structure of the model and to overlay the results of analyses and simulations); Biotechnology Units, (BU, fine tuning the YsiC for specific applications); Integrated (Macro)Units (IMU, with both computing and experimental competence)

Experimental data collection: A common protocol and yeast genetic background(s) will be used so that, for each relevant module, quantitative estimations that can ultimately be fed into a single model will be made. These estimations will mainly include number and/or concentration, modification, localisation and interaction of molecules and activity levels. A common set of defined experimental conditions including both steady state growth on different nutrients (in a chemostat as well as in shake flasks), and perturbed and differentiation conditions including nutritional shift-up and shift-down, environmental stresses (oxidative, heat, osmotic) will be defined. Centrifugal elutriation or synchronisation protocols will be used to reduce the complexity of the population under study. Ultimately an extensive set of system data (transcriptome, proteome, including major post-translational modifications such as phosphorylation, protein/protein and protein/nucleic acid interaction maps, metabolome, rRNA and ribosomal protein level), as well as specific data required for each module (kinetic constants for enzymes, protein/protein and protein/nucleic acid interaction as determined by high resolution techniques such as BIAcore, NMR, FRET) will be collected on the very same cells for each condition.

It is estimated that at any one time 30-40 groups may be enrolled and contribute their expertise in major scientific areas indicated below or introducing newly developed relevant technological platforms to the IP.

Nutrient and ion transport;

Nutrient signaling;

Carbon metabolism;

Stable RNA synthesis and accumulation;

mRNA synthesis and degradation;

Protein synthesis;

Protein degradation (ubiquination);

Protein phosphorylation;

Protein glycosylation and other post-translational modifications;

Protein sorting and secretion;

Assembly of high-order structures (spindles, kinetochores…);

Cell cycle;


Aging and apoptosis;

Mathematical modelling;

Metabolic control analysis;

Flux analysis;

Partial differential equations;


Database management;

Web based communication and representation.


Figure 2 Schematic organisation of the IP


This EoI is presented by the groups indicated below. They have extensive experimental as well as computational experience with systems biology in budding yeast. They could staff the two macro-units A and B of Figure 2.

Integrated Macro Unit A

Milano – Lilia Alberghina, co-coordinator (and coordinator of the EoI). Molecular biology, physiology and biochemistry of the coordination between growth and cell cycle in yeast. Systems Biology approach to the regulation of yeast growth and cell cycle. Experience in coordination of EC network and in national and European science policy committees.

Leuven – Johan Thevelein. Molecular genetics and biochemistry of yeast signal transduction, identification of nutrient-sensing and novel signalling components for activation of the cAMP-PKA and related signaling pathways.; research group selected as new department of the Flemish Interuniversity Institute of Biotechnology.

StuttgartMatthias Reuss. Signal induced dynamics of yeast central carbon metabolism. Experimental observations and modelling of cell cycle and energy metabolism. Modelling of various modules for the yeast cell like transcription, mRNA degradation, translation, folding and proteolysis.

Integrated Macro Unit B

Amsterdam Hans V. Westerhoff, co-coordinator. Molecular cell physiology and silicon biochemistry of yeast glycolysis energetics and transport. Westerhoff here represents a team of groups of the BioCentrum Amsterdam, the Technical University of Delft and two biotech industries that collaborate on yeast

Göteborg Stefan Hohmann. It is the mission of the Göteborg Yeast Centre with its ten groups and sixty researchers to contribute to a complete, systems level understanding of the yeast cell. The Centre employs tools of global gene and protein expression analysis, metabolomics, front-line microscopy and cell physiology. The Centre will be one node in the upcoming national systems biology initiative

Oxford David Fell. Development of scalable, modular simulation software in a high-level language from a current, open-source metabolic analysis and simulation package; definition of model description standards; analysis and parameter estimation of enzyme kinetic data; model building and simulation; structural analysis of modules to ensure network integrity and consistency; maintenance of a network server distributing software, module library etc.

Scientists interested in the IP are invited to send Prof. Lilia Alberghina a brief outline of the research they would carry out whilst bearing strictly in mind the requirements of the molecular systems biology approach described here.