Alignment of microbial fitness with engineered product formation: Obligatory coupling between acetate production and photoautotrophic growth

Wei Du, Joeri A. Jongbloets, C. van Boxtel, Hugo Pineda Hernández, David Lips, B.G. Olivier, Klaas J. Hellingwerf, Filipe Branco dos Santos

Research output: Contribution to journalArticle

Abstract

Background: Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. Results: In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline - FRUITS - that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. Conclusions: This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.

LanguageEnglish
Article number38
Pages1-13
Number of pages13
JournalBiotechnology for Biofuels
Volume11
Issue number38
DOIs
StatePublished - 13 Feb 2018

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acetate
Acetates
fitness
Cyanobacteria
production system
Biomass
cyanobacterium
metabolite
Growth
bioengineering
Synechocystis
Bioengineering
productivity
biomass
Human Development
Metabolites
Metabolic Networks and Pathways
Computer Simulation
genome
Pipelines

Keywords

  • Acetate production
  • Cyanobacteria
  • Growth coupled
  • Metabolic modeling
  • Strain stability

Cite this

Du, Wei ; Jongbloets, Joeri A. ; van Boxtel, C. ; Hernández, Hugo Pineda ; Lips, David ; Olivier, B.G. ; Hellingwerf, Klaas J. ; dos Santos, Filipe Branco. / Alignment of microbial fitness with engineered product formation : Obligatory coupling between acetate production and photoautotrophic growth. In: Biotechnology for Biofuels. 2018 ; Vol. 11, No. 38. pp. 1-13
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Alignment of microbial fitness with engineered product formation : Obligatory coupling between acetate production and photoautotrophic growth. / Du, Wei; Jongbloets, Joeri A. ; van Boxtel, C.; Hernández, Hugo Pineda; Lips, David ; Olivier, B.G.; Hellingwerf, Klaas J.; dos Santos, Filipe Branco.

In: Biotechnology for Biofuels, Vol. 11, No. 38, 38, 13.02.2018, p. 1-13.

Research output: Contribution to journalArticle

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T1 - Alignment of microbial fitness with engineered product formation

T2 - Biotechnology for Biofuels

AU - Du,Wei

AU - Jongbloets,Joeri A.

AU - van Boxtel,C.

AU - Hernández,Hugo Pineda

AU - Lips,David

AU - Olivier,B.G.

AU - Hellingwerf,Klaas J.

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KW - Cyanobacteria

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KW - Metabolic modeling

KW - Strain stability

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