Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

Abstract Background Methanotrophs is a promising biocatalyst in biotechnological applications with their ability to utilize single carbon (C1) feedstock to produce high-value compounds. Understanding the behavior of biological networks of methanotrophic bacteria in different parameters is vital to s...

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Main Authors: Anh Duc Nguyen, Gayoung Nam, Donghyuk Kim, Eun Yeol Lee
Format: Article
Language:English
Published: BMC 2020-06-01
Series:Microbial Cell Factories
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12934-020-01382-5
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author Anh Duc Nguyen
Gayoung Nam
Donghyuk Kim
Eun Yeol Lee
author_facet Anh Duc Nguyen
Gayoung Nam
Donghyuk Kim
Eun Yeol Lee
author_sort Anh Duc Nguyen
collection DOAJ
description Abstract Background Methanotrophs is a promising biocatalyst in biotechnological applications with their ability to utilize single carbon (C1) feedstock to produce high-value compounds. Understanding the behavior of biological networks of methanotrophic bacteria in different parameters is vital to systems biology and metabolic engineering. Interestingly, methanotrophic bacteria possess the pyrophosphate-dependent 6-phosphofructokinase (PPi-PFK) instead of the ATP-dependent 6-phosphofructokinase, indicating their potentials to serve as promising model for investigation the role of inorganic pyrophosphate (PPi) and PPi-dependent glycolysis in bacteria. Gene knockout experiments along with global-omics approaches can be used for studying gene functions as well as unraveling regulatory networks that rely on the gene product. Results In this study, we performed gene knockout and RNA-seq experiments in Methylotuvimicrobium alcaliphilum 20Z to investigate the functional roles of PPi-PFK in C1 metabolism when cells were grown on methane and methanol, highlighting its metabolic importance in C1 assimilation in M. alcaliphilum 20Z. We further conducted adaptive laboratory evolution (ALE) to investigate regulatory architecture in pfk knockout strain. Whole-genome resequencing and RNA-seq approaches were performed to characterize the genetic and metabolic responses of adaptation to pfk knockout. A number of mutations, as well as gene expression profiles, were identified in pfk ALE strain to overcome insufficient C1 assimilation pathway which limits the growth in the unevolved strain. Conclusions This study first revealed the regulatory roles of PPi-PFK on C1 metabolism and then provided novel insights into mechanism of adaptation to the loss of this major metabolic enzyme as well as an improved basis for future strain design in type I methanotrophs.
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spelling doaj.art-2126a4d0bc07472c9ad69bcc9c801a332022-12-22T00:59:41ZengBMCMicrobial Cell Factories1475-28592020-06-0119111410.1186/s12934-020-01382-5Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20ZAnh Duc Nguyen0Gayoung Nam1Donghyuk Kim2Eun Yeol Lee3Department of Chemical Engineering, Kyung Hee UniversitySchool of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST)School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST)Department of Chemical Engineering, Kyung Hee UniversityAbstract Background Methanotrophs is a promising biocatalyst in biotechnological applications with their ability to utilize single carbon (C1) feedstock to produce high-value compounds. Understanding the behavior of biological networks of methanotrophic bacteria in different parameters is vital to systems biology and metabolic engineering. Interestingly, methanotrophic bacteria possess the pyrophosphate-dependent 6-phosphofructokinase (PPi-PFK) instead of the ATP-dependent 6-phosphofructokinase, indicating their potentials to serve as promising model for investigation the role of inorganic pyrophosphate (PPi) and PPi-dependent glycolysis in bacteria. Gene knockout experiments along with global-omics approaches can be used for studying gene functions as well as unraveling regulatory networks that rely on the gene product. Results In this study, we performed gene knockout and RNA-seq experiments in Methylotuvimicrobium alcaliphilum 20Z to investigate the functional roles of PPi-PFK in C1 metabolism when cells were grown on methane and methanol, highlighting its metabolic importance in C1 assimilation in M. alcaliphilum 20Z. We further conducted adaptive laboratory evolution (ALE) to investigate regulatory architecture in pfk knockout strain. Whole-genome resequencing and RNA-seq approaches were performed to characterize the genetic and metabolic responses of adaptation to pfk knockout. A number of mutations, as well as gene expression profiles, were identified in pfk ALE strain to overcome insufficient C1 assimilation pathway which limits the growth in the unevolved strain. Conclusions This study first revealed the regulatory roles of PPi-PFK on C1 metabolism and then provided novel insights into mechanism of adaptation to the loss of this major metabolic enzyme as well as an improved basis for future strain design in type I methanotrophs.http://link.springer.com/article/10.1186/s12934-020-01382-5Adaptive laboratory evolutionC1 assimilationMethanotrophPyrophosphate-linked phosphofructokinasePyrophosphate metabolism
spellingShingle Anh Duc Nguyen
Gayoung Nam
Donghyuk Kim
Eun Yeol Lee
Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
Microbial Cell Factories
Adaptive laboratory evolution
C1 assimilation
Methanotroph
Pyrophosphate-linked phosphofructokinase
Pyrophosphate metabolism
title Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
title_full Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
title_fullStr Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
title_full_unstemmed Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
title_short Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
title_sort metabolic role of pyrophosphate linked phosphofructokinase pfk for c1 assimilation in methylotuvimicrobium alcaliphilum 20z
topic Adaptive laboratory evolution
C1 assimilation
Methanotroph
Pyrophosphate-linked phosphofructokinase
Pyrophosphate metabolism
url http://link.springer.com/article/10.1186/s12934-020-01382-5
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