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Abstract: Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and 13C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes. [ABSTRACT FROM AUTHOR]

Promoters adjust cellular gene expression in response to internal or external signals and are key elements for implementing dynamic metabolic engineering concepts in fermentation processes. One useful signal is the dissolved oxygen content of the culture medium, since production phases often proceed in anaerobic conditions. Although several oxygen-dependent promoters have been described, a comprehensive and comparative study is missing. The goal of this work is to systematically test and characterize 15 promoter candidates that have been previously reported to be induced upon oxygen depletion in Escherichia coli. For this purpose, we developed a microtiter plate-level screening using an algal oxygen-independent flavin-based fluorescent protein and additionally employed flow cytometry analysis for verification. Various expression levels and dynamic ranges could be observed, and six promoters (nar-strong, nar-medium, nar-weak, nirB-m, yfiD-m, and fnrF8) appear particularly suited for dynamic metabolic engineering applications. We demonstrate applicability of these candidates for dynamic induction of enforced ATP wasting, a metabolic engineering approach to increase productivity of microbial strains that requires a narrow level of ATPase expression for optimal function. The selected candidates exhibited sufficient tightness under aerobic conditions while, under complete anaerobiosis, driving expression of the cytosolic F 1 -subunit of the ATPase from E. coli to levels that resulted in unprecedented specific glucose uptake rates. We finally utilized the nirB-m promoter to demonstrate the optimization of a two-stage lactate production process by dynamically enforcing ATP wasting, which is automatically turned on in the anaerobic (growth-arrested) production phase to boost the volumetric productivity. Our results are valuable for implementing metabolic control and bioprocess design concepts that use oxygen as signal for regulation and induction. [Display omitted] • 15 oxygen-dependent promoters systematically characterized. • Microtiter plate level screening using an oxygen-independent LOV fluorescent reporter. • Verification of expression levels and dynamic ranges using flow cytometry. • Six most suitable promoters for dynamic metabolic engineering applications identified. • Example study: nirB-m driven ATP wasting boosts lactate productivity in a two-stage process. [ABSTRACT FROM AUTHOR]

Abstract: Some agents, including Escherichia coli and group A Streptococcus pyogenes cause infections in oxygen depleted sites. LL-37 is a human host defence peptide shown previously to play an important role in controlling infections caused by these bacteria. However, the effect of oxygen levels on the antimicrobial activity of LL-37 remains obscure. In order to test the effect of oxygen (or lack thereof) on LL-37's activity against E. coli and S. pyogenes, a method for adapting commonly used microtiter plates for real-time growth-kinetic (and growth-inhibition) measurements under anaerobic conditions was developed. Using the proposed method, anaerobic conditions were attained in the microplate within 30 min and were maintained for at least five days. Anaerobiosis was further confirmed by comparing the growth of two anaerobic oral species (Porphyromonas gingivalis and Fusobacterium nucleatum) in anaerobic compartments of microtiter plates versus aerobic ones. Both species grew only in the anaerobic compartments of the plates as indicated by the growth curves generated. The sensitivities of E. coli and S. pyogenes to LL-37 were tested under anaerobic conditions and compared to those in aerobic ones. The oxygen facultative E. coli grew to a higher density under aerobic conditions and its sensitivity to LL-37 was increased under anaerobiosis. The microaerophilic pathogen S. pyogenes grew faster and to a higher density under anaerobic conditions and was much more resistant to LL-37 under oxygen deprivation. Our results suggest that resistance to antimicrobial agents of microbes infecting anaerobic-microaerophilic sites should be tested under oxygen-restricted conditions. [Copyright &y& Elsevier]

Highlights: [•] Escherichia coli contains two l-asparaginase isozymes with distinct localization, kinetics and regulation. [•] Mutant strains were used to examine the roles of these enzymes in l-asparagine utilization. [•] We report that l-asparaginase II permits growth on asparagine and glycerol under anaerobic conditions. [•] We propose that this enzyme is the first step in a co-regulated pathway leading to fumarate. [•] The pathway is regulated by anaerobiosis and cAMP and provides a terminal elector acceptor. [ABSTRACT FROM AUTHOR]

Abstract: The aim of this work was to understand the steps controlling the biotransformation of trimethylammonium compounds into l(-)-carnitine by Escherichia coli. The high-cell density reactor steady-state levels of carbon source (glycerol), biotransformation substrate (crotonobetaine), acetate (anaerobiosis product) and fumarate (as an electron acceptor) were pulsed by increasing them fivefold. Following the pulse, the evolution of the enzyme activities involved in the biotransformation process of crotonobetaine into l(-)-carnitine (crotonobetaine hydration), in the synthesis of acetyl-CoA (ACS: acetyl-CoA synthetase and PTA: ATP: acetate phosphotransferase) and in the distribution of metabolites for the tricarboxylic acid (ICDH: isocitrate dehydrogenase) and glyoxylate (ICL: isocitrate lyase) cycles was monitored. In addition, the levels of carnitine, the cell ATP content and the NADH/NAD+ ratio were measured in order to assess the importance and participation of these energetic coenzymes in the catabolic system. The results provided an experimental demonstration of the important role of the glyoxylate shunt during biotransformation and the need for high levels of ATP to maintain metabolite transport and biotransformation. Moreover, the results obtained for the NADH/NAD+ pool indicated that it is correlated with the biotransformation process at the NAD+ regeneration and ATP production level in anaerobiosis. More importantly, a linear correlation between the NADH/NAD+ ratio and the levels of the ICDH and ICL (carbon and electron flows) and the PTA and ACS (acetate and ATP production and acetyl-CoA synthesis) activity levels was assessed. The main metabolic pathway operating during cell metabolic perturbation with a pulse of glycerol and acetate in the high-cell density membrane reactor was that related to ICDH and ICL, both regulating the carbon metabolism, together with PTA and ACS enzymes (regulating ATP production). [Copyright &y& Elsevier]