Biology subjects

Kugler, A.

Publications and source records attributed to Kugler, A..

2 recordsLinked to original sources

bioRxiv2023

Machine learning predicts system-wide metabolic flux control in cyanobacteria

Metabolic fluxes and their control mechanisms are fundamental in cellular metabolism, offering insights for the study of biological systems and biotechnological applications. However, quantitative and predictive understanding of controlling biochemical reactions in microbial cell factories, especially at the system level, is limited. In this work, we present ARCTICA, a computational framework that integrates constraint-based modelling with machine learning tools to address this challenge. Using the model cyanobacterium Synechocystis sp. PCC 6803 as chassis, we demonstrate that ARCTICA effectively simulates global-scale metabolic flux control. Key findings are that (i) the photosynthetic bioproduction is mainly governed by enzymes from the Calvin-Benson-Bassham (CBB) cycle, rather than by those involve in the biosynthesis of the end-product, (ii) the catalytic capacity of the CBB cycle limits the photosynthetic activity and downstream pathways and (iii) ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a major, but not the most, limiting step in the CBB cycle. Predicted metabolic reactions qualitatively align with prior experimental observations, validating our modelling approach. ARCTICA serves as a valuable pipeline for understanding cellular physiology and predicting rate-limiting steps in genome-scale metabolic networks, providing guidance for bioengineering of cyanobacteria. HighlightsO_LIA workflow for flux control analysis in Synechocystis sp. PCC 6803. C_LIO_LIMachine learning with features derived from genome-scale metabolic modelling. C_LIO_LIIdentification of potential key reactions for metabolic adaptations and cell bioengineering. C_LI

systems biology↗

bioRxiv2022

Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria represent an attractive platform for the sustainable production of chemicals and fuels. However, the obtained rates, yields, and titers are below those required for commercial application. Carbon metabolism alone cannot achieve maximal accumulation of end-products, since an efficient production of target molecules entails energy and redox balance, in addition to carbon flow. The interplay between cofactor regeneration and heterologous metabolite overproduction in cyanobacteria is not fully explored. Here, we applied stoichiometric metabolic modelling of the cyanobacterium Synechocystis sp. PCC 6803, in order to investigate the optimality of energy and redox metabolism, while overproducing bio-alkenes - isobutene, isoprene, ethylene and 1-undecene. Our network-wide analysis indicates that the rate of NADP+ reduction, rather than ATP synthesis, controls ATP/NADPH ratio, and thereby chemical production. The simulation implies that energy and redox balance necessitates gluconeogenesis, and that acetate metabolism via phosphoketolase serves as an efficient carbon- and energy-recycling pathway. Furthermore, we show that an auxiliary pathway, composed of serine, one-carbon and glycine metabolism, supports cellular redox homeostasis and ATP cycling, and that the Synechocystis metabolism is controlled by few key reactions carrying a high flux. The study also revealed non-intuitive metabolic pathways to enhance isoprene, ethylene and 1-undecene production. We conclude that metabolism of ATP and NAD(P)H is entwined with carbon and nitrogen metabolism, and cannot be assessed in isolation. We envision that the presented here in-depth metabolic analysis will guide the a priori design of Synechocystis as a host strain for an efficient manufacturing of target products.

systems biology↗