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Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus

View ORCID ProfileShany Ofaim, View ORCID ProfileSnorre Sulheim, View ORCID ProfileEivind Almaas, Daniel Sher, View ORCID ProfileDaniel Segrè
doi: https://doi.org/10.1101/2020.07.20.211680
Shany Ofaim
1Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, USA
2Department of Marine Biology, University of Haifa, Haifa, Israel
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Snorre Sulheim
1Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, USA
3Department of Biotechnology and Food Science, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
4Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
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Eivind Almaas
3Department of Biotechnology and Food Science, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
5K.G. Jebsen Center for Genetic Epidemiology, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
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Daniel Sher
2Department of Marine Biology, University of Haifa, Haifa, Israel
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Daniel Segrè
1Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, USA
6Department of Biomedical Engineering, Boston University, Boston, MA
7Department of Physics and Department of Biology, Boston University, MA
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  • For correspondence: dsegre@bu.edu
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Abstract

Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner-Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 20, 2020.
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Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus
Shany Ofaim, Snorre Sulheim, Eivind Almaas, Daniel Sher, Daniel Segrè
bioRxiv 2020.07.20.211680; doi: https://doi.org/10.1101/2020.07.20.211680
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Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus
Shany Ofaim, Snorre Sulheim, Eivind Almaas, Daniel Sher, Daniel Segrè
bioRxiv 2020.07.20.211680; doi: https://doi.org/10.1101/2020.07.20.211680

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