One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

Abstract

bIn cells, N 10 -formyltetrahydrofolate (N 10 -fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N 10 -fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (⌬folD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N 10 -fTHF in the ⌬folD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N 10 -fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The ⌬folD strain (harboring fhs on the chromosome) showed a high NADP ؉ -to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.T he pathway of one-carbon metabolism is central to the synthesis of purine nucleotides, thymidylate, glycine, and methionine (Fig. 1). The enzymes that catalyze interconversions of the pathway intermediates are highly conserved across the three domains of life (1-6). Serine hydroxymethyltransferase (GlyA) catalyzes the reversible reaction of conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene-tetrahydrofolate (5,10-CH 2 -THF) (7). FolD, a bifunctional enzyme, carries out sequential steps of reversible conversions of 5,10-CH 2 -THF to 5,10-methenyltetrahydrofolate (5,10-CH ϩ -THF), followed by the conversion of the latter to N 10 -formyltetrahydrofolate (N 10 -fTHF) by its dehydrogenase and cyclohydrolase activities, respectively (8). Availability of N 10 -fTHF is crucial for the de novo pathway of purine nucleotide biosynthesis and formylation of the initiator tRNA (tRNA fMet ) to initiate protein synthesis in eubacteria and eukaryotic organelles (9). N 10 -fTHF can also be synthesized by formyltetrahydrofolate synthetase, Fhs (also known as formate-tetrahydrofolate ligase), by utilizing THF, formate, and ATP (Fig. 1). The dual scheme of N 10 -fTHF synthesis is conserved in eukaryotes and some archaea (6). Many eukaryotic organisms possess FolD with trifunctional activities of dehydrogenase-cyclohydrolase-synthetase (10, 11). Among eubacter...

Deep sequencing of biofilm microbiomes on dental composite materials

“…However, in direct tests, carolacton has only been shown to inhibit certain isolates of S. pneumoniae [27] and does not affect the growth of most bacteria, including S. mutans at neutral or higher pH [10]. Resistance mechanisms have evolved such as the alternative enzyme Fhs, which is especially widespread in anaerobic bacteria [28], and the efflux pumps which most bacteria possess [26,27,29]. The strong effect of carolacton on S. mutans biofilm viability was always striking because it only occurs at low pH [30], reflecting the essential role of FolD in acid survival of S. mutans [31].…”

Enhancement of Bioremediation and Phytoremediation Using Electrokinetics

“…1. Genetic engineering can be used to enhance the outcome of bioremediation through changing or rewiring of microorganism metabolic pathways so as to enhance the ability of bacteria in degrading the targeted contaminant [21,22]. Also, modifying bacterial genes and regulatory networks to make them tougher to survive and tolerate high contaminant concentration in soils [23].…”

Benzoate-TolerantEscherichia coliStrains from Experimental Evolution Lose the Gad Regulon, Multi-Drug Efflux Pumps, and Hydrogenases

“…Other genes that had early, persistent mutations include folD (5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase, for thymidine biosynthesis) (50) in population A1; and apt (adenosine phosphoribosyltransferase, for purine salvage) (51) in population A5. A 6-bp insertion upstream of apt was found by generation 500 in population A5 and persisted through generation 2,000; and a frameshift in apt coding sequence was in strain E1-5 ( Table S2 ).…”