CyanoDesign - A web-based tool for the generation and analysis of in silico mutants for Synechocystis sp. PCC 6803

Autores UPV
Año
CONGRESO CyanoDesign - A web-based tool for the generation and analysis of in silico mutants for Synechocystis sp. PCC 6803

Abstract

CyanoFactory is an European research project whose main interest is to develop strategies to enhance the production of renewable energy and biofuels. Within this project, the nodes of Mittweida and Valencia have several tasks, one of which is to make use of techniques of systems biology and synthetic biology to improve hydrogen production of organism Synechocystis sp. PCC 6803. As part of this project, we have participated in the development of CyanoDesign, which is a web-based tool that allows, mainly, the study of the flux distribution over the metabolic network and the generation and evaluation of in silico mutants. This environment is suitable for the design and integration of parts and devices into a cyanobacterial chassis aimed at increase H2 production in Synechocystis. It also permits to characterize different strains in terms of the metabolic behaviour. CyanoDesign is based in part inPyNetMet[1] that allows the detection of reactions fully disconnected in the network of a metabolic model. These reactions can later be updated, corrected or deleted by the user. It also permits the inclusion of metabolites that only appear once in the whole metabolism. CyanoDesign uses the information from a knowledge database called CyanoFactoryKB inspired in the model of WholleCellKB [2]. This information enables CyanoDesign to generate numerical simulations that can be used to assist experimental design of growth media. In particular, it has permitted us to improve the metabolic model iSyn811 of Synechocystis sp. PCC 6803 given in [3]. References: 1. Gamermann D., Montagud A., Jaime Infante R.A., Triana J., Urchueguía J.F., and Fernández de Córdoba P., PyNetMet: Python tools for efficient work with networks and metabolic models, Comput. Math. Biol., 3 (2014) 1-11. 2. Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. WholeCellKB: Pathway/Genome Databases for Comprehensive Whole-Cell Models.41,D787-D792(2013) 3. Montagud A., Zelezniak A., Navarro E., Fernández de Córdoba P., Urchueguía J.F., and Patil K.R. Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803, Biotechnol. J. 6 (2011) 330-342.