Applications of stable isotope‐based metabolomics and fluxomics toward synthetic biology of cyanobacteria

Abstract

Unique features of cyanobacteria (e.g., photosynthesis and nitrogen fixation) make them potential candidates for production of biofuels and other value‐added biochemicals. As prokaryotes, they can be readily engineered using synthetic and systems biology tools. Metabolic engineering of cyanobacteria for the synthesis of desired compounds requires in‐depth knowledge of central carbon and nitrogen metabolism, pathway fluxes, and their regulation. Metabolomics and fluxomics offer the comprehensive analysis of metabolism by directly characterizing the biochemical activities of cells. This information is acquired by measuring the abundance of key metabolites and their rates of interconversion, which can be achieved by labeling cells with stable isotopes, quantifying metabolite pool sizes and isotope incorporation by gas chromatography/liquid chromatography‐mass spectrometry GC/LC‐MS or nuclear magnetic resonance (NMR), and mathematical modeling to estimate in vivo metabolic fluxes. Herein, we review progress that has been made to adapt metabolomics and fluxomics tools to examine model cyanobacterial species. We summarize the application of metabolic flux analysis (MFA) strategies to identify metabolic bottlenecks that can be targeted to boost cell growth, improve stress tolerance, or enhance biochemical production in cyanobacteria. Despite the advances in metabolomics, fluxomics, and other synthetic and systems biology tools during the past years, further efforts are required to increase our understanding of cyanobacterial metabolism in order to create efficient photosynthetic hosts for the production of value‐added compounds. This article is categorized under: Laboratory Methods and Technologies > Metabolomics Biological Mechanisms > Metabolism Analytical and Computational Methods > Analytical Methods

Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways

“…Different analytical tools and approaches in fluxomics have been reviewed recently ( Wiechert et al, 2007 ; Niittylae et al, 2009 ; Klein and Heinzle, 2012 ; Winter and Krömer, 2013 ; Niedenführ et al, 2015 ). Even if different analytical tools are utilized in fluxomics/metabolomics research, nuclear magnetic resonance (NMR) spectroscopy ( Giraudeau, 2020 ) and mass spectrometry (MS) ( Wiechert et al, 2007 ; Choi and Antoniewicz, 2019 ; Babele and Young, 2020 ) are the most commonly used tools in metabolomic studies.…”

A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers

“…Unfortunately, metabolic flux distribution of neither Anabaena 33047 nor any other heterocyst forming cyanobacteria is available. 13 C-MFA-based intracellular flux estimates are available only for a few non-heterocystous cyanobacteria [ 69 ]. Among these, only Synechococcus 7002 occupies a marine habitat as Anabaena 33047 [ 70 ].…”

NMR and Metabolomics—A Roadmap for the Future

“…NMR-based fluxomics can exploit the ability of NMR to easily localize the exact position of a given (labeled) atom in a specific molecule. The spatial localization of specific 13 C or 2 H isotopes incorporated within a specific metabolite can provide a clear indication of the enzymes or pathways used to generate that metabolite [ 75 , 76 ]. Isotope labeling allows NMR-based fluxomics to easily link metabolites to proteins and pathways.…”