Biosynthesis of methanofuran in Methanobacterium thermoautotrophicum

On the evolution of coenzyme biosynthesis

Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.

Biosynthesis of the 5-(Aminomethyl)-3-furanmethanol moiety of methanofuran

We have established the biosynthetic pathway and the associated genes for the biosynthesis of the 5-(aminomethyl)-3-furanmethanol (F1) moiety of methanofuran in the methanogenic archaeon Methanocaldococcus jannaschii. The recombinant enzyme, derived from the MJ1099 gene, was shown to readily condense glyceraldehyde 3-phosphate (Ga-3P) and dihydroxyacetone-P (DHAP) to form 4-(hydroxymethyl)-2-furancarboxaldehyde phosphate (4-HFC-P). The recombinant purified pyridoxal 5'-phosphate-dependent aminotransferase, derived from the MJ0684 gene, was found to be specific for catalyzing the transamination reaction between 4-HFC-P and [(15)N]alanine to produce [(15)N] 5-(aminomethyl)-3-furanmethanol-P (F1-P) and pyruvate. To confirm these results in cell extracts, we developed sensitive analytical methods for the liquid chromatography-ultraviolet-electrospray ionization mass spectrometry analysis of F1 as a 7-nitrobenzofurazan derivative. This method has allowed for the quantitation of trace amounts of F1 and F1-P in cell extracts and the measurement of the incorporation of stable isotopically labeled precursors into F1. After incubation of cell extracts with [1,2,3-(13)C3]pyruvate and DHAP, 4-([(2)H2]hydroxymethyl)-2-furancarboxylic acid phosphate (4-HFCA-P) or 4-([(2)H2]hydroxymethyl)-2-furancarboxaldehyde phosphate (4-HFC-P) was found to be incorporated into F1-P. 4-HFCA-P and 4-HFC-P were confirmed in cell extracts after removal of the phosphate. The low level of incorporation of [1,2,3-(13)C3]pyruvate into F1-P in these experiments is explained by the fact that the labeled pyruvate must first be converted into Ga-3-P through gluconeogenesis before being incorporated into 4-HFC-P. Cell extracts incubated with 4-HFC-P and a mixture of [(15)N]aspartate, [(15)N]glutamate, and [(15)N]alanine produced [(15)N]F1-P. We also demonstrated that aqueous solutions of methylglyoxal or pyruvate heated with dihydroxyacetone led to the formation of 4-HFC and 4-HFCA, suggesting a possible prebiotic route to this moiety of methanofuran.

Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746

Methanosarcina barkeri is an Archaeon that produces methane anaerobically as the primary byproduct of its metabolism. M. barkeri can utilize several substrates for ATP and biomass production including methanol, acetate, methyl amines, and a combination of hydrogen and carbon dioxide. In 2006, a metabolic reconstruction of M. barkeri, iAF692, was generated based on a draft genome annotation. The iAF692 reconstruction enabled the first genome-Scale simulations for Archaea. Since the publication of the first metabolic reconstruction of M. barkeri, additional genomic, biochemical, and phenotypic data have clarified several metabolic pathways. We have used this newly available data to improve the M. barkeri metabolic reconstruction. Modeling simulations using the updated model, iMG746, have led to increased accuracy in predicting gene knockout phenotypes and simulations of batch growth behavior. We used the model to examine knockout lethality data and make predictions about metabolic regulation under different growth conditions. Thus, the updated metabolic reconstruction of M. barkeri metabolism is a useful tool for predicting cellular behavior, studying the methanogenic lifestyle, guiding experimental studies, and making predictions relevant to metabolic engineering applications.

Biosynthesis of the methanogenic cofactors

Our current knowledge of the pathways and genes involved in the biosynthesis of the methanogenic coenzymes methanopterin, coenzyme B, methanofuran, coenzyme F420, and coenzyme M is presented. Proposed reaction mechanisms for several of the novel reactions involved in the pathways are presented.

Halotolerance of Methanobacterium thermoautotrophicum delta H and Marburg

Methanobacterium thermoautotrophicum delta H and Marburg were adapted to grow in medium containing up to 0.65 M NaCl. From 0.01 to 0.5 M NaCl, there was a lag before cell growth which increased with increasing external NaCl. The effect of NaCl on methane production was not significant once the cells began to grow. Intracellular solutes were monitored by nuclear magnetic resonance (NMR) spectroscopy as a function of osmotic stress. In the delta H strain, the major intracellular small organic solutes, cyclic-2,3-diphosphoglycerate and glutamate, increased at most twofold between 0.01 and 0.4 M NaCl and decreased when the external NaCl was 0.5 M. M. thermoautotrophicum Marburg similarly showed a decrease in solute (cyclic-2,3-diphosphoglycerate, 1,3,4,6-tetracarboxyhexane, and L-alpha-glutamate) concentrations for cells grown in medium containing > 0.5 M NaCl. At 0.65 M NaCl, a new organic solute, which was visible in only trace amounts at the lower NaCl concentrations, became the dominant solute. Intracellular potassium in the delta H strain, detected by atomic absorption and 39K NMR, was roughly constant between 0.01 and 0.4 M and then decreased as the external NaCl increased further. The high intracellular K+ was balanced by the negative charges of the organic osmolytes. At the higher external salt concentrations, it is suggested that Na+ and possibly Cl- ions are internalized to provide osmotic balance. A striking difference of strain Marburg from strain delta H was that yeast extract facilitated growth in high-NaCl-containing medium. The yeast extract supplied only trace NMR-detectable solutes (e.g., betaine) but had a large effect on endogenous glutamate levels, which were significantly decreased. Exogenous choline and glycine, instead of yeast extract, also aided growth in NaCl-containing media. Both solutes were internalized with the choline converted to betaine; the contribution to osmotic balance of these species was 20 to 25% of the total small-molecule pool. These results indicate that M. thermoautotrophicum shows little changes in its internal solutes over a wide range of external NaCl. Furthermore, they illustrate the considerable differences in physiology in the delta H and Marburg strains of this organism.

Identification, Biosynthesis, and Function of 1,3,4,6-Hexanetetracarboxylic Acid in Methanobacterium thermoautotrophicum ΔH

An unusual compound, 1,3,4,6-hexanetetracarboxylic acid, was identified by 1 H and 13 C two-dimensional nuclear magnetic resonance spectroscopy and gas chromatography-mass spectrometry as one of the major components of the small-molecule pool in Methanobacterium thermoautotrophicum ΔH under optimal conditions of cell growth. Incorporation of 13 C- and 2 H-labeled acetates was consistent with the biosynthesis of this tetracarboxylic acid from α-ketoglutarate, two molecules of acetyl-coenzyme A, and one molecule of CO 2 , as established for the tetracarboxylic acid moiety of methanofuran. 13 CO 2 pulse- 12 CO 2 chase methodology was used to establish the turnover rate for this compound. In contrast to the two other major solutes in this bacterium, cyclic 2,3-diphosphoglycerate and glutamate, which are key metabolic intermediates, this free tetracarboxylic acid was metabolically inactive, with a half-life that exceeded the cell doubling time. Hence, this molecular pool cannot serve as a metabolic intermediate in cell biosynthesis. The functional role of free tetracarboxylate as a conservative part of a system that maintains high positive internal osmotic pressure in this bacterium is proposed.