Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i>
Hexanoic acid and its derivatives have been recently recognized as value-added materials and can be synthesized by several microbes. Of them, <i>Megasphaera elsdenii</i> has been considered as an interesting hexanoic acid producer because of its capability to utilize a variety of carbons...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2020-04-01
|
Series: | Microorganisms |
Subjects: | |
Online Access: | https://www.mdpi.com/2076-2607/8/4/539 |
id |
doaj-0503c8df86924c7d947aa78e03f41d7a |
---|---|
record_format |
Article |
spelling |
doaj-0503c8df86924c7d947aa78e03f41d7a2020-11-25T02:28:44ZengMDPI AGMicroorganisms2076-26072020-04-01853953910.3390/microorganisms8040539Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i>Na-Rae Lee0Choong Hwan Lee1Dong-Yup Lee2Jin-Byung Park3Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, KoreaDepartment of Bioscience and Biotechnology, Konkuk University, Seoul 05029, KoreaSchool of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, KoreaDepartment of Food Science and Engineering, Ewha Womans University, Seoul 03760, KoreaHexanoic acid and its derivatives have been recently recognized as value-added materials and can be synthesized by several microbes. Of them, <i>Megasphaera elsdenii</i> has been considered as an interesting hexanoic acid producer because of its capability to utilize a variety of carbons sources. However, the cellular metabolism and physiology of <i>M. elsdenii</i> still remain uncharacterized. Therefore, in order to better understand hexanoic acid synthetic metabolism in <i>M. elsdenii</i>, we newly reconstructed its genome-scale metabolic model, <i>i</i>ME375, which accounts for 375 genes, 521 reactions, and 443 metabolites. A constraint-based analysis was then employed to evaluate cell growth under various conditions. Subsequently, a flux ratio analysis was conducted to understand the mechanism of bifurcated hexanoic acid synthetic pathways, including the typical fatty acid synthetic pathway via acetyl-CoA and the TCA cycle in a counterclockwise direction through succinate. The resultant metabolic states showed that the highest hexanoic acid production could be achieved when the balanced fractional contribution via acetyl-CoA and succinate in reductive TCA cycle was formed in various cell growth rates. The highest hexanoic acid production was maintained in the most perturbed flux ratio, as phosphoenolpyruvate carboxykinase (<i>pck</i>) enables the bifurcated pathway to form consistent fluxes. Finally, organic acid consuming simulations suggested that succinate can increase both biomass formation and hexanoic acid production.https://www.mdpi.com/2076-2607/8/4/539<i>Megasphaera elsdenii</i>hexanoic acidbifurcated pathwaygenome-scale metabolic modelconstraint-based modeling |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Na-Rae Lee Choong Hwan Lee Dong-Yup Lee Jin-Byung Park |
spellingShingle |
Na-Rae Lee Choong Hwan Lee Dong-Yup Lee Jin-Byung Park Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i> Microorganisms <i>Megasphaera elsdenii</i> hexanoic acid bifurcated pathway genome-scale metabolic model constraint-based modeling |
author_facet |
Na-Rae Lee Choong Hwan Lee Dong-Yup Lee Jin-Byung Park |
author_sort |
Na-Rae Lee |
title |
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i> |
title_short |
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i> |
title_full |
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i> |
title_fullStr |
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i> |
title_full_unstemmed |
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing <i>Megasphaera elsdenii</i> |
title_sort |
genome-scale metabolic network reconstruction and in silico analysis of hexanoic acid producing <i>megasphaera elsdenii</i> |
publisher |
MDPI AG |
series |
Microorganisms |
issn |
2076-2607 |
publishDate |
2020-04-01 |
description |
Hexanoic acid and its derivatives have been recently recognized as value-added materials and can be synthesized by several microbes. Of them, <i>Megasphaera elsdenii</i> has been considered as an interesting hexanoic acid producer because of its capability to utilize a variety of carbons sources. However, the cellular metabolism and physiology of <i>M. elsdenii</i> still remain uncharacterized. Therefore, in order to better understand hexanoic acid synthetic metabolism in <i>M. elsdenii</i>, we newly reconstructed its genome-scale metabolic model, <i>i</i>ME375, which accounts for 375 genes, 521 reactions, and 443 metabolites. A constraint-based analysis was then employed to evaluate cell growth under various conditions. Subsequently, a flux ratio analysis was conducted to understand the mechanism of bifurcated hexanoic acid synthetic pathways, including the typical fatty acid synthetic pathway via acetyl-CoA and the TCA cycle in a counterclockwise direction through succinate. The resultant metabolic states showed that the highest hexanoic acid production could be achieved when the balanced fractional contribution via acetyl-CoA and succinate in reductive TCA cycle was formed in various cell growth rates. The highest hexanoic acid production was maintained in the most perturbed flux ratio, as phosphoenolpyruvate carboxykinase (<i>pck</i>) enables the bifurcated pathway to form consistent fluxes. Finally, organic acid consuming simulations suggested that succinate can increase both biomass formation and hexanoic acid production. |
topic |
<i>Megasphaera elsdenii</i> hexanoic acid bifurcated pathway genome-scale metabolic model constraint-based modeling |
url |
https://www.mdpi.com/2076-2607/8/4/539 |
work_keys_str_mv |
AT naraelee genomescalemetabolicnetworkreconstructionandinsilicoanalysisofhexanoicacidproducingimegasphaeraelsdeniii AT choonghwanlee genomescalemetabolicnetworkreconstructionandinsilicoanalysisofhexanoicacidproducingimegasphaeraelsdeniii AT dongyuplee genomescalemetabolicnetworkreconstructionandinsilicoanalysisofhexanoicacidproducingimegasphaeraelsdeniii AT jinbyungpark genomescalemetabolicnetworkreconstructionandinsilicoanalysisofhexanoicacidproducingimegasphaeraelsdeniii |
_version_ |
1724836863854772224 |