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The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16

Arenas-López, Christian; Locker, Jessica; Orol, Diego; Walter, Frederik; Busche, Tobias; Kalinowski, Jörn; Minton, Nigel P.; Kovács, Katalin; Winzer, Klaus


Christian Arenas-López

Jessica Locker

Diego Orol

Frederik Walter

Tobias Busche

Jörn Kalinowski

Professor of Appliedmolecular Microbiology


3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this study, the native 3-HP metabolism of Cupriavidus necator was investigated and manipulated as it represents a promising chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2.

When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy, a highly undesirable trait in the context of biological 3-HP production which required elimination. Inactivation of the methylcitrate pathway needed for propionate utilisation did not affect the organism’s ability to grow on 3-HP. Putative genes involved in 3-HP degradation were identified by bioinformatics means and confirmed by transcriptomic analyses, the latter revealing considerably increased expression in the presence of 3-HP. Genes identified in this manner encoded three putative (methyl)malonate semialdehyde dehydrogenases (mmsA1, mmsA2 and mmsA3) and two putative dehydrogenases (hpdH and hbdH). These genes, which are part of three separate mmsA operons, were inactivated through deletion of the entire coding region, either singly or in various combinations, to engineer strains unable to grow on 3-HP. Whilst inactivation of single genes or double deletions could only delay but not abolish growth, a triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain was unable utilise 3-HP as the sole source of carbon and energy. Under the used conditions this strain was also unable to co–metabolise 3-HP alongside other carbon and energy sources such as fructose and CO2/H2. Further analysis suggested primary roles for the different mmsA operons in the utilisation of β-alanine generating substrates (mmsA1), degradation of 3-HP (mmsA2), and breakdown of valine (mmsA3).

Three different (methyl)malonate semialdehyde dehydrogenases contribute to 3-HP breakdown in C. necator H16. The created triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain represents an ideal chassis for autotrophic 3-HP production.


Arenas-López, C., Locker, J., Orol, D., Walter, F., Busche, T., Kalinowski, J., …Winzer, K. (2019). The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. Biotechnology for Biofuels, 12,

Journal Article Type Article
Acceptance Date Jun 6, 2019
Online Publication Date Jun 17, 2019
Publication Date Jun 17, 2019
Deposit Date Jun 17, 2019
Publicly Available Date Jun 18, 2019
Journal Biotechnology for Biofuels
Electronic ISSN 1754-6834
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 12
Article Number 150
Keywords 3-Hydroxypropionic acid, metabolic engineering, Cupriavidus necator, Ralstonia eutropha, co-metabolism, carbon fixation, malonate semialdehyde dehydrogenase, β-alanine, valine
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Additional Information Received: 12 April 2019; Accepted: 7 June 2019; First Online: 17 June 2019; : The full transcriptomic dataset generated and analysed during the current study is available in the ArrayExpress repository (ExternalRef removed) and is accessible under E-MTAB-7701.; : Not applicable.; : Not applicable.; : The authors declare that they have no competing interests.


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