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Systems biology techniques show high prevalence of post-translational regulation in the cyanobacterium Synechocystis PCC 6803

Time: Fri 2021-12-17 09.00

Location: Kollegiesalen, Brinellvägen 8, Stockholm

Language: English

Subject area: Biotechnology

Doctoral student: Jan Karlsen , Systembiologi, Science for Life Laboratory, SciLifeLab

Opponent: Professor Martin Hagemann, Universität Rostock

Supervisor: Associate Professor Elton Paul Hudson, Skolan för kemi, bioteknologi och hälsa (CBH)

QC 2021-11-24

Abstract

Earth's climate has been upset by carbon dioxide (CO2) emissions from human activities and the use of fossil resources. To prevent catastrophic events on the environment and on civilizations, we urgently need to develop alternative solutions that utilize renewable resources. One contributing solution is to exploit metabolically engineered cyanobacteria that convert CO2 and sunlight into bioproducts, such as fuels or biodegradable plastics. However, these ancient bacteria have evolved a complex, robust, and self-regulated metabolic network that efficiently converts CO2 to biomass rather than a foreign chemical, which limits the productivity of engineered strains and the potential to use them in an industrial setting. Extended knowledge is therefore needed regarding the regulatory processes that govern their metabolism, in order to develop more efficient producer strains. The present investigation took advantage of recently developed systems biology techniques to explore translational and post-translational regulation in the model cyanobacterium Synechocystis. The first study showed that CO2-starved Synechocystis downregulated anabolic processes by post-translational ribosome inactivation. Ribosome profiling indicated that ribosomes that remained active were primarily synthesizing proteins involved in CO2 uptake and stress mediation. The regulatory protein thioredoxin TrxC was upregulated by induced translation and may conduct post-translational redox regulation during CO2 stress. In the second study, diurnal oscillations in the transcriptome, translatome and proteome were investigated using mRNA sequencing, ribosome profiling and quantitative proteomics. A stable proteome was observed, despite significant oscillations in protein synthesis. A model describing the dynamic relationship between protein synthesis and protein abundance suggested that a slow protein turnover is causing the observed effect. A stable proteome suggests that shifts between autotrophic and heterotrophic metabolism occurring during day-night cycles are controlled by post-translational regulation. The third study investigated proteome arrangement strategies during light and CO2 limitation. Integration of proteomics data into a cellular protein economy model indicated that Synechocystis keeps underutilized protein reserves. These reserves may be activated by post-translational regulation to quickly adapt to changing growth conditions. In the fourth study, post-translational regulation by metabolite interactions was investigated using interaction proteomics and enzyme kinetic assays. Glyceraldehyde-3-phosphate activated the enzyme fructose/sedoheptulose-bisphosphatase, suggesting a feedforward activation mechanism in the Calvin cycle. AMP deactivates the same enzyme, which may facilitate glycogen catabolism during CO2 starvation. The findings and data of this work could guide future studies and attempts to engineer cyanobacteria for a sustainable production of commodity chemicals.

urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-305282

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