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In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform

The advent of genome scale metabolic models of Escherichia coli coupled with limited successes in computational advancement could facilitate rapid advancement in the field of metabolic engineering and synthetic biology. E. coli has been subjected to various metabolic engineering approaches using est...

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Main Authors: Mienda, Bashir Sajo, Omar, Mohd. Shahir Shamsir, Mohd. Salleh, Faezah
Format: Article
Published: Aizeon Publishers 2014
Subjects:
Q Science (General)
TP Chemical technology
Online Access:http://eprints.utm.my/id/eprint/59792/
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spelling my.utm.597922022-04-24T02:34:49Z http://eprints.utm.my/id/eprint/59792/ In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform Mienda, Bashir Sajo Omar, Mohd. Shahir Shamsir Mohd. Salleh, Faezah Q Science (General) TP Chemical technology The advent of genome scale metabolic models of Escherichia coli coupled with limited successes in computational advancement could facilitate rapid advancement in the field of metabolic engineering and synthetic biology. E. coli has been subjected to various metabolic engineering approaches using established experimental methods to produce D-lactate under micro-aerobic conditions using glycerol as substrate. However, investigation on the in silico prediction and/or deletion of competing pathway genes on glycerol for the production of D-lactate by E. coli genome scale model using regulatory on or off minimization (ROOM) under the OptFlux software platform is yet to be elucidated. Here, we show that in silico metabolic engineering using this software platform by simulating the knocking out of pyruvate formate lyase (pflB/b0903), fumarate reductase (frdA/b4154), phosphoacetyltransferase (pta/b2297) and alcohol/acetaldehyde dehydrogenase (adhE/b1241) have been predicted to increase D-lactate production in E. coli. The mutant models constructed in this study exhibited growth rate that is 96 % of the wild-type model, and hence maintaining a significant flux for D-lactate production. The results reported herein, were found to be in conformity with previously established experimental studies. These findings indicates that the OptFlux software platform using ROOM as simulation algorithm hold great promise as potential software platform that can accurately predict metabolic engineering targets to guide future experimental studies not only for D-lactate production in E. coli but also for other microbial chemical compounds of interests. Aizeon Publishers 2014 Article PeerReviewed Mienda, Bashir Sajo and Omar, Mohd. Shahir Shamsir and Mohd. Salleh, Faezah (2014) In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform. International Journal of Computational Bioinformatics and in Silico Modeling, 3 (4). pp. 460-465. ISSN 2320-0634
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
topic Q Science (General)
TP Chemical technology
spellingShingle Q Science (General)
TP Chemical technology
Mienda, Bashir Sajo
Omar, Mohd. Shahir Shamsir
Mohd. Salleh, Faezah
In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform
description The advent of genome scale metabolic models of Escherichia coli coupled with limited successes in computational advancement could facilitate rapid advancement in the field of metabolic engineering and synthetic biology. E. coli has been subjected to various metabolic engineering approaches using established experimental methods to produce D-lactate under micro-aerobic conditions using glycerol as substrate. However, investigation on the in silico prediction and/or deletion of competing pathway genes on glycerol for the production of D-lactate by E. coli genome scale model using regulatory on or off minimization (ROOM) under the OptFlux software platform is yet to be elucidated. Here, we show that in silico metabolic engineering using this software platform by simulating the knocking out of pyruvate formate lyase (pflB/b0903), fumarate reductase (frdA/b4154), phosphoacetyltransferase (pta/b2297) and alcohol/acetaldehyde dehydrogenase (adhE/b1241) have been predicted to increase D-lactate production in E. coli. The mutant models constructed in this study exhibited growth rate that is 96 % of the wild-type model, and hence maintaining a significant flux for D-lactate production. The results reported herein, were found to be in conformity with previously established experimental studies. These findings indicates that the OptFlux software platform using ROOM as simulation algorithm hold great promise as potential software platform that can accurately predict metabolic engineering targets to guide future experimental studies not only for D-lactate production in E. coli but also for other microbial chemical compounds of interests.
format Article
author Mienda, Bashir Sajo
Omar, Mohd. Shahir Shamsir
Mohd. Salleh, Faezah
author_facet Mienda, Bashir Sajo
Omar, Mohd. Shahir Shamsir
Mohd. Salleh, Faezah
author_sort Mienda, Bashir Sajo
title In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform
title_short In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform
title_full In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform
title_fullStr In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform
title_full_unstemmed In silico metabolic engineering prediction of Escherichia coli genome model for production of D-lactic acid from glycerol using the OptFlux software platform
title_sort in silico metabolic engineering prediction of escherichia coli genome model for production of d-lactic acid from glycerol using the optflux software platform
publisher Aizeon Publishers
publishDate 2014
url http://eprints.utm.my/id/eprint/59792/
_version_ 1732945378981969920
score 13.211869

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