Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential

• Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified. 

Ämnesord

NATURVETENSKAP  -- Biologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

Nyckelord

E. coli

Max-min driving force analysis

Network-embedded thermodynamic analysis

Pathway enumeration

Pathway thermodynamics

Synechocystis

Amino acids

Biochemistry

Biosynthesis

Carbon

Escherichia coli

Metabolism

Metabolites

Thermoanalysis

Thermodynamic properties

Driving force analysis

Thermo dynamic analysis

Thermodynamics

2 oxoglutaric acid

acetyl coenzyme A

adenosine triphosphate

coenzyme A

erythrose 4 phosphate

ferulic acid

fructose 6 phosphate

fumaric acid

glyceraldehyde 3 phosphate

glyceraldehyde 3 phosphate dehydrogenase

isoprenoid

lysine

malate dehydrogenase

malic acid

naringenin

nicotinamide adenine dinucleotide

nicotinamide adenine dinucleotide (phosphate) transhydrogenase

oxaloacetic acid

phosphate

reduced nicotinamide adenine dinucleotide phosphate

succinate coenzyme A ligase

succinate dehydrogenase

tricarboxylic acid

unclassified drug

Article

comparative study

computer analysis

concentration process

controlled study

enzyme synthesis

glycolysis

metabolic engineering

metabolomics

nonhuman

photorespiration

photosynthesis

priority journal

prospecting optimal pathway with python

workflow

Publikations- och innehållstyp

ref (ämneskategori)

art (ämneskategori)