An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

Isabella Casini; Tim McCubbin; Sofia Esquivel-Elizondo; Guillermo G Luque; Daria Evseeva; Christian Fink; Sebastian Beblawy; Nicholas D Youngblut; Ludmilla Aristilde; Daniel H Huson; Andreas Dräger; Ruth E Ley; Esteban Marcellin; Largus T Angenent; Bastian Molitor

doi:10.1016/j.isci.2023.108016

An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

iScience. 2023 Sep 22;26(10):108016. doi: 10.1016/j.isci.2023.108016. eCollection 2023 Oct 20.

Authors

Isabella Casini¹, Tim McCubbin^{2

3

4}, Sofia Esquivel-Elizondo⁵, Guillermo G Luque⁵, Daria Evseeva^{6

7}, Christian Fink¹, Sebastian Beblawy¹, Nicholas D Youngblut⁵, Ludmilla Aristilde⁸, Daniel H Huson^{6

7

9}, Andreas Dräger^{6

7

9}, Ruth E Ley^{5

9}, Esteban Marcellin^{2

3

4}, Largus T Angenent^{1

9

10

11

12}, Bastian Molitor^{1

9}

Affiliations

¹ Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany.
² Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
³ Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia.
⁴ ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia.
⁵ Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany.
⁶ Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
⁷ Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.
⁸ Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA.
⁹ Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
¹⁰ AG Angenent, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany.
¹¹ Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark.
¹² The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark.

Abstract

Methanogenesis allows methanogenic archaea to generate cellular energy for their growth while producing methane. Thermophilic hydrogenotrophic species of the genus Methanothermobacter have been recognized as robust biocatalysts for a circular carbon economy and are already applied in power-to-gas technology with biomethanation, which is a platform to store renewable energy and utilize captured carbon dioxide. Here, we generated curated genome-scale metabolic reconstructions for three Methanothermobacter strains and investigated differences in the growth performance of these same strains in chemostat bioreactor experiments with hydrogen and carbon dioxide or formate as substrates. Using an integrated systems biology approach, we identified differences in formate anabolism between the strains and revealed that formate anabolism influences the diversion of carbon between biomass and methane. This finding, together with the omics datasets and the metabolic models we generated, can be implemented for biotechnological applications of Methanothermobacter in power-to-gas technology, and as a perspective, for value-added chemical production.

Keywords: Genetic engineering; Proteomics; Systems biology.