, 14:96 | Cite as

Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis

  • Sastia Prama PutriEmail author
  • Yasumune Nakayama
  • Claire Shen
  • Shingo Noguchi
  • Katsuaki Nitta
  • Takeshi Bamba
  • Sammy Pontrelli
  • James Liao
  • Eiichiro Fukusaki
Original Article



Previously constructed Escherichia coli strains that produce 1-propanol use the native threonine pathway, or a heterologous citramalate pathway. However, based on the energy and cofactor requirements of each pathway, a combination of the two pathways produces synergistic effects that increase the theoretical maximum yield with a simultaneous unexplained increase in productivity.


Identification of key factors that contribute to synergistic effect leading to 1-propanol yield and productivity improvement in E. coli with native threonine pathway and heterologous citramalate pathway.


A combination of snapshot metabolomic profiling and dynamic metabolic turnover analysis were used to identify system-wide perturbations that contribute to the productivity improvement.

Result and Conclusion

In the presence of both pathways, increased glucose consumption and elevated levels of glycolytic intermediates are attributed to an elevated phosphoenolpyruvate (PEP)/pyruvate ratio that is known to increase the function of the native phosphotransferase. Turnover analysis of nitrogen containing byproducts reveals that ammonia assimilation, required for the threonine pathway, is streamlined when provided with an NAD(P)H surplus in the presence of the citramalate pathway. Our study illustrates the application of metabolomics in identification of factors that alter cellular physiology for improvement of 1-propanol bioproduction.


Escherichia coli 1-Propanol Synergy Metabolic profiling Mass spectrometry Metabolic turnover analysis 



Gas chromatography-quadrupole/mass spectrometry


Principal component analysis


Limit of detection


Limit of quantitation


Principal component



This research was fully supported by Japan Science and Technology (JST), Strategic International Collaborative Research Program, SICORP for JP-US Metabolomics and National Science Foundation (NSF) MCB-1139318.

Author contributions

SPP designed the study, performed the metabolome analysis and data analysis, and drafted the manuscript. YN performed the turnover analysis and data analysis and helped to draft the manuscript. CS supplied all the strains used in this study, and assisted with the interpretation of metabolome analysis results. SN participated in the metabolome and turnover analysis and data analysis. TB advised the selection of analytical platform, and provided assistance on metabolome analysis and data processing. KN participated in the manuscript preparation, data analysis and data interpretation. SP aided in data interpretation and writing of the manuscript. JL participated in the design of the study, coordination and writing of the manuscript. EF conceived of the study, and participated in its design and coordination. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Research involving human and animal rights

This article does not contain any studies with human participants or animals performed by any of authors.

Supplementary material

11306_2018_1386_MOESM1_ESM.docx (272 kb)
Supplementary material 1 (DOCX 271 KB)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Sastia Prama Putri
    • 1
    Email author
  • Yasumune Nakayama
    • 1
    • 2
  • Claire Shen
    • 3
    • 6
  • Shingo Noguchi
    • 1
    • 4
  • Katsuaki Nitta
    • 1
  • Takeshi Bamba
    • 1
    • 5
  • Sammy Pontrelli
    • 6
  • James Liao
    • 6
  • Eiichiro Fukusaki
    • 1
  1. 1.Department of Biotechnology, Graduate School of EngineeringOsaka UniversityOsakaJapan
  2. 2.Department of Applied Microbial TechnologySojo UniversityKumamotoJapan
  3. 3.Department of Chemical EngineeringNational Tsing Hua UniversityHsinchuTaiwan, Republic of China
  4. 4.Drug Metabolism & Pharmacokinetics Research Laboratories, R&D DivisionDaiichi Sankyo Co., Ltd., Shinagawa R&D CenterTokyoJapan
  5. 5.Research Center for Transomics Medicine, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
  6. 6.Department of Chemical and Biomolecular EngineeringUniversity of California, Los AngelesLos AngelesUSA

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