Available online at www.sciencedirect.com Modular model-based design for heterologous bioproduction in bacteria Thomas E Landrain 1,* , Javier Carrera 1,2,3,* , Boris Kirov 1,* , Guillermo Rodrigo 1,2,* and Alfonso Jaramillo 1,4 We review the current status of expression of heterologous systems for bioenergy and bioproduction in bacteria using a model-based approach. As an aim for synthetic biology, it requires mathematical models of genetic modules that could be characterized independently of their context. This fastens the design of metabolic circuits using a combinatorial design approach, where given pathways could be optimized for maximal bioproduction, while being nontoxic for the chassis. We show how recent characterization of genetic parts, such as promoters, RBS or sRNAs could be used to fine-tune the expression of individual genes to achieve that goal. We also present lists of enzymes that are used for bioproduction, enlarging such set of biological parts. Addresses 1 Synth-Bio group. Epigenomics Project, Universite ´ d’E ´ vry Val d’Essonne-Genopole-CNRS UPS3201, 91034 E ´ vry, France 2 Instituto de Biologı´a Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientı´ficas-UPV, 46022 Vale ` ncia, Spain 3 Instituto ITACA, Universidad Polite ´ cnica de Valencia, 46022 Vale ` ncia, Spain 4 Laboratoire de Biochimie, E ´ cole Polytechnique-CNRS UMR7654, 91128 Palaiseau, France Corresponding author: Jaramillo, Alfonso (alfonso.jaramillo@polytechnique.fr) * These authors have contributed equally to this work. Current Opinion in Biotechnology 2009, 20:272–279 This review comes from a themed issue on Energy biotechnology Edited by Peter Lindblad and Thomas Jeffries Available online 24th June 2009 0958-1669/$ – see front matter # 2009 Elsevier Ltd. All rights reserved. DOI 10.1016/j.copbio.2009.06.003 Introduction Bacteria have been widely studied and well characterized because of their simplicity to be used as organism models. The ability of synthesizing target organic compounds using such microbes is of particular interest for biotech- nology. One way the field of metabolic engineering pursues this goal [1] is by expressing heterologous enzymes forming a given metabolic pathway linked to bacterial metabolism. With the advent of new high- throughput techniques, genome-scale models have been developed which have allowed an extension of the field in recent years [2  ]. Those models provide very useful information to properly design the new metabolic pro- gram. In addition, we need to develop appropriate models for the heterologous genetic systems that we introduce into a given host. As those models have to be valid in all the contexts where they could be used, it is very convenient to aim for a modular approach, where the model for each module is independent of how it is assembled to other modules. This allows the combina- torial exploration of many models. There have been some advances on using models for biological parts (see http://partsregistry.org), such as promoters, ribo- some binding sites (RBSs), RNAs, or coding sequences such as enzymes. In this review we will focus on the use of models for such elements to predict the cell behavior and ultimately aid in the design of optimal metabolic path- ways for bioproduction. The use of regulatory elements is pivotal to the appropriate expression of heterologous enzymes. Transcriptional regu- lation, by means of promoters, controls enzyme expression and thus all biochemical processes are catalyzed by enzymes. Some of the best-studied promoters in rokar- yotes and in particular E. coli are the carbohydrate utiliz- ation systems [3]. Their heterologous use, by using appropriate knockout strains, is very attractive for biopro- duction since it provides the opportunity of strong reliable control over the promoter activity through factors that are or could easily be made totally independent of the cellular internal state. Alternatively, gene expression could be regulated post-transcriptionally, by using engineered RBSs and riboswitches. In addition, synthetic riboswitches engineered from natural templates, open the door to a reliable tunability of cell processes with external molecules [4]. In the present work we will review the recent research on characterizing such elements by integrating the data into suitable models and their possible combinations pro- viding predictable results that could facilitate the engin- eering of bioproduction pathways in bacteria. We will also discuss the various enzymes that have successfully been used in heterologous expression of metabolic pathways in bacteria. Characterized parts for successful metabolic pathway expression Promoter elements Promoters are one of the keys for successfully directing the bioprocesses within the living cell and thus, con- trolling bioproduction. The biochemical characterization Current Opinion in Biotechnology 2009, 20:272–279 www.sciencedirect.com