Awakening a latent carbon fixation cycle in<i>Escherichia coli</i>

Satanowski, Ari; Dronsella, Beau; Noor, Elad; Vögeli, Bastian; He, Hai; Wichmann, Philipp; Erb, Tobias J.; Lindner, Steffen N.; Bar‐Even, Arren

doi:10.1101/2020.05.18.102244

Cited by 6 publications

(4 citation statements)

References 86 publications

(112 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Computational analysis to identify glycolytic bypasses in E. coli. In order to identify possible pathways that can bypass EMP glycolysis resorting to native E. coli enzymes only we used a system analysis approach based on the genome-scale metabolic model of this bacterium (50). The approach is described in detail in the supplementary method.…”

Section: Methodsmentioning

confidence: 99%

Activating silent glycolysis bypasses inEscherichia coli

Marx

Hoenick

Biletskaia

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal, the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal immediately operated in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary for implementing a functional methylglyoxal pathway. Furthermore, we engineered the ‘serine shunt’ which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection we performed an adaptive laboratory evolution study using an enolase deletion strain. The evolved mutants were shown to use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.

show abstract

Section: Methodsmentioning

confidence: 99%

Activating silent glycolysis bypasses inEscherichia coli

Marx

Hoenick

Biletskaia

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The energy and carbon metabolism consists of particular central pathways which are highly preserved across the variety of bacterial species, regardless of the wide variety of growth substrates and conditions they utilize (Sudarsan et al, 2014). Certain conserved central reactions are almost universally present in many species for provision of carbon frameworks for biosynthesis (Satanowski et al, 2020). Bacterial energy requirements are met by substrate level phosphorylation reactions, along with the membrane bound ATPase and the transmembrane proton gradient (Kakinuma, 1998).…”

Section: Carbon and Energy Metabolismmentioning

confidence: 99%

Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria

et al. 2023

View full text Add to dashboard Cite

The growth and survival of an organism in a particular environment is highly depends on the certain indispensable genes, termed as essential genes. Sulfate-reducing bacteria (SRB) are obligate anaerobes which thrives on sulfate reduction for its energy requirements. The present study used Oleidesulfovibrio alaskensis G20 (OA G20) as a model SRB to categorize the essential genes based on their key metabolic pathways. Herein, we reported a feedback loop framework for gene of interest discovery, from bio-problem to gene set of interest, leveraging expert annotation with computational prediction. Defined bio-problem was applied to retrieve the genes of SRB from literature databases (PubMed, and PubMed Central) and annotated them to the genome of OA G20. Retrieved gene list was further used to enrich protein–protein interaction and was corroborated to the pangenome analysis, to categorize the enriched gene sets and the respective pathways under essential and non-essential. Interestingly, the sat gene (dde_2265) from the sulfur metabolism was the bridging gene between all the enriched pathways. Gene clusters involved in essential pathways were linked with the genes from seleno-compound metabolism, amino acid metabolism, secondary metabolite synthesis, and cofactor biosynthesis. Furthermore, pangenome analysis demonstrated the gene distribution, where 69.83% of the 116 enriched genes were mapped under “persistent,” inferring the essentiality of these genes. Likewise, 21.55% of the enriched genes, which involves specially the formate dehydrogenases and metallic hydrogenases, appeared under “shell.” Our methodology suggested that semi-automated text mining and network analysis may play a crucial role in deciphering the previously unexplored genes and key mechanisms which can help to generate a baseline prior to perform any experimental studies.

show abstract

“…Reactions were to a large extent set to be reversible, with exceptions such as exchange reactions and reactions known to operate only in the forward direction, such as RUBISCO. Avoiding reaction direction constraints prior to thermodynamic analysis was recently shown to be crucial in finding carbon fixation pathways in E. coli (Satanowski et al, 2020). The total number of feasible EFMs leading to either biomass, PHB, or both, can be taken as a measure for the flexibility of the metabolic network.…”

Section: Network Flexibility In C Necator Is High On Fructose and Low...mentioning

confidence: 99%

Thermodynamic limitations of metabolic strategies for PHB production from formate and fructose in Cupriavidus necator

Janasch

Crang

Bruch

et al. 2022

Preprint

View full text Add to dashboard Cite

The chemolithotroph Cupriavidus necator H16 is known as a natural producer of the bioplastic-polymer PHB, as well as for its metabolic versatility to utilize different substrates, including formate as the sole carbon and energy source. Depending on the entry point of the substrate, this versatility requires adjustment of the thermodynamic landscape to maintain sufficiently high driving forces for biological processes. Here we employed a model of the core metabolism of C. necator H16 to analyze the thermodynamic driving forces and PHB yields of different metabolic engineering strategies. For this, we enumerated elementary flux modes (EFMs) of the network and evaluated their PHB yields as well as thermodynamics via Max-min driving force (MDF) analysis and random sampling of driving forces. A heterologous ATP:citrate lyase reaction was predicted to increase driving force for producing acetyl-CoA. A heterologous phosphoketolase reaction was predicted to increase maximal PHB yields as well as driving forces. These enzymes were verified experimentally to enhance PHB titers between 60 and 300% in select conditions. The EFM analysis also revealed that metabolic strategies for PHB production from formate may be limited by low driving forces through citrate lyase and aconitase, as well as cofactor balancing, and identified reactions of the core metabolism associated with low and high PHB yield. The findings of this study aid in understanding metabolic adaptation. Furthemore, the outlined approach will be useful in designing metabolic engineering strategies in other non-model bacteria.

show abstract

Awakening a latent carbon fixation cycle inEscherichia coli

Cited by 6 publications

References 86 publications

Activating silent glycolysis bypasses inEscherichia coli

Activating silent glycolysis bypasses inEscherichia coli

Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria

Thermodynamic limitations of metabolic strategies for PHB production from formate and fructose in Cupriavidus necator

Contact Info

Product

Resources

About