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Pathways Analyzer: Design of a Tool for the Synthetic Assembly of Escherichia Coli K-12 MG1655 Bacteria for Biofuel Production

Laura Vasquez, Ricardo Alvarado, Allan Orozco
doi: https://doi.org/10.1101/634998
Laura Vasquez
1Department of Computer Engineering, Costa Rica Institute of Technology (TEC), Cantoblanco, Madrid, Spain
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Ricardo Alvarado
2National Laboratory of Nanotechnology (LANOTEC), Nanobiotechnology Department, Cantoblanco, Madrid, Spain
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Allan Orozco
3School of Health Technology, Faculty of Medicine, University of Costa Rica (UCR), Cantoblanco, Madrid, Spain
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  • For correspondence: allan.orozcosolano@ucr.ac.cr
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ABSTRACT

Summary Due to the impact of environmental pollution, the importance of producing high quality biofuels and to leverage organic waste that normally would have no use has increased over time. Through synthetic biology, it is possible to improve existing organisms to process waste that is traditionally not used for biofuel production, such as whey.

With the redesign of metabolic pathways, it is possible to create connections for the implementation of new organisms that carry out functions that are normally not present in nature.

From a computational point of view, metabolic pathways, which can be found in data sources as KEGG, can be converted to a graph data structure. These transformations enable the use of well-known algorithms, which enables the optimization of the analyses required to achieve the assembly of new organisms.

The present work aims to design a tool for the transformation of metabolic pathways and the development of path finding algorithms that establish relevant links between compounds that are essential to the biofuel production process.

As a result, a catalog of biobricks is created from the analysis of a subset of paths which can be used in the design stage of the synthetic assembly of the E. coli bacteria. The assembly’s structure and functions are characterized according to the pieces used.

Finally, new constructions are visualized with the goal of demonstrating and supporting the analysis processes, thus assisting people that work in the field of Synthetic Biology.

Availability Pathways Analyzer is accessible at: https://gitlab.com/lvasquezcr/pathways-analyzer/

Footnotes

  • lvasquez{at}ic-itcr.ac.cr, ralvarado{at}cenat.ac.cr, allan.orozcosolano{at}ucr.ac.cr

  • https://gitlab.com/lvasquezcr/pathways-analyzer

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 19, 2019.
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Pathways Analyzer: Design of a Tool for the Synthetic Assembly of Escherichia Coli K-12 MG1655 Bacteria for Biofuel Production
Laura Vasquez, Ricardo Alvarado, Allan Orozco
bioRxiv 634998; doi: https://doi.org/10.1101/634998
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Pathways Analyzer: Design of a Tool for the Synthetic Assembly of Escherichia Coli K-12 MG1655 Bacteria for Biofuel Production
Laura Vasquez, Ricardo Alvarado, Allan Orozco
bioRxiv 634998; doi: https://doi.org/10.1101/634998

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