Metabolism of L-glyceraldehyde 3-phosphate in Escherichia coli

Metabolomic Profiling Analysis of Physiological Responses to Acute Hypoxia and Reoxygenation in Juvenile Qingtian Paddy Field Carp Cyprinus Carpio Var Qingtianensis

The Qingtian paddy field carp (Cyprinus carpio var qingtianensis) is a local carp cultivated in the rice field of Qingtian county, Zhejiang province, China. The paddy field environment is distinct from the pond environment. Due to the inability to artificially increase oxygen, the dissolved oxygen greatly changes during the day. Therefore, investigating the physiological regulation to the changes of acute dissolved oxygen in Qingtian paddy field carp (PF-carp) will dramatically clarify how it adapts to the paddy breeding environment. The high tolerance of Qingtian paddy field carp to hypoxia makes it an ideal organism for studying molecular regulatory mechanisms during hypoxia process and reoxygenation following hypoxia in fish. In this study, we compared the changes of metabolites in the hepatopancreas during hypoxia stress and the following reoxygenation through comparative metabolomics. The results showed 131 differentially expressed metabolites between the hypoxic groups and control groups. Among them, 95 were up-regulated, and 36 were down-regulated. KEGG Pathway enrichment analysis showed that these differential metabolites were mainly involved in regulating lipid, protein, and purine metabolism PF-carps could require energy during hypoxia by enhancing the gluconeogenesis pathway with core glutamic acid and glutamine metabolism. A total of 63 differentially expressed metabolites were screened by a comparison between the reoxygenated groups and the hypoxic groups. Specifically, 15 were up-regulated, and 48 were down-regulated. The KEGG Pathway enrichment analysis supported that PF-carp could continue to gain energy by consuming glutamic acid and the glutamine accumulated during hypoxia and simultaneously weaken the ammonia-transferring effect of amino acids and the toxicity of ammonia. By consuming glycerophospholipids and maintaining the Prostaglandin E content, cell damage was improved, sphingosinol synthesis was reduced, and apoptosis was inhibited. Additionally, it could enhance the salvage synthesis and de novo synthesis of purine, reduce purine accumulation, promote the synthesis of nucleotide and energy carriers, and assist in recovering physiological metabolism. Overall, results explained the physiological regulation mechanism of PF-carp adapting to the acute changes of dissolved oxygen at the metabolic level and also provided novel evidence for physiological regulation of other fish in an environment with acute changes in dissolved oxygen levels.

An L-glucose catabolic pathway in Paracoccus species 43P

BACKGROUND

L-Glucose, the enantiomer of D-glucose, was believed not to be utilized by any organisms.

RESULTS

An L-glucose-utilizing bacterium was isolated, and its L-glucose catabolic pathway was identified genetically and enzymatically.

CONCLUSION

L-Glucose was utilized via a novel pathway to pyruvate and D-glyceraldehyde 3-phosphate.

SIGNIFICANCE

This might lead to an understanding of homochirality in sugar metabolism. An L-glucose-utilizing bacterium, Paracoccus sp. 43P, was isolated from soil by enrichment cultivation in a minimal medium containing L-glucose as the sole carbon source. In cell-free extracts from this bacterium, NAD(+)-dependent L-glucose dehydrogenase was detected as having sole activity toward L-glucose. This enzyme, LgdA, was purified, and the lgdA gene was found to be located in a cluster of putative inositol catabolic genes. LgdA showed similar dehydrogenase activity toward scyllo- and myo-inositols. L-Gluconate dehydrogenase activity was also detected in cell-free extracts, which represents the reaction product of LgdA activity toward L-glucose. Enzyme purification and gene cloning revealed that the corresponding gene resides in a nine-gene cluster, the lgn cluster, which may participate in aldonate incorporation and assimilation. Kinetic and reaction product analysis of each gene product in the cluster indicated that they sequentially metabolize L-gluconate to glycolytic intermediates, D-glyceraldehyde-3-phosphate, and pyruvate through reactions of C-5 epimerization by dehydrogenase/reductase, dehydration, phosphorylation, and aldolase reaction, using a pathway similar to L-galactonate catabolism in Escherichia coli. Gene disruption studies indicated that the identified genes are responsible for L-glucose catabolism.

The diversity of microbial aldo/keto reductases from Escherichia coli K12

The genome of Escherichia coli K12 contains 9 open reading frames encoding aldo/keto reductases (AKRs) that are differentially regulated and sequence diverse. A significant amount of data is available for the E. coli AKRs through the availability of gene knockouts and gene expression studies, which adds to the biochemical and kinetic data. This together with the availability of crystal structures for nearly half of the E. coli AKRs and homologues of several others provides an opportunity to look at the diversity of these representative bacterial AKRs. Based around the common AKR fold of (β/α)8 barrel with two additional α-helices, the E. coli AKRs have a loop structure that is more diverse than their mammalian counterparts, creating a variety of active site architectures. Nearly half of the AKRs are expected to be monomeric, but there are examples of dimeric, trimeric and octameric enzymes, as well as diversity in specificity for NAD as well as NADP as a cofactor. However in functional assignments and characterisation of enzyme activities there is a paucity of data when compared to the mammalian AKR enzymes.

Restoring a metabolic pathway

Gluconeogenesis is blocked in a strain of Escherichia coli that is deficient in triosephosphate isomerase, but it was restored by the insertion of a plasmid coding for an L-glyceraldehyde 3-phosphate reductase (YghZ). This reductase provides a "bypass" that produces dihydroxyacetone phosphate (DHAP) by the consecutive enzyme-catalyzed reduction of L-glyceraldehyde 3-phosphate ( L-GAP) by NADPH to give L-glycerol 3-phosphate and reoxidation by NAD(+) catalyzed by endogenous L-glycerol 3-phosphate dehydrogenase to give DHAP. The origin of cellular L-GAP remains to be determined.

A metabolic bypass of the triosephosphate isomerase reaction

Triosephosphate isomerase (TIM) catalyzes the interconversion of d-glyceraldehyde 3-phosphate and dihydroxyacetone phosphate, an essential step in glycolytic and gluconeogenic metabolism. To uncover promiscuous isomerases embedded within the Escherichia coli genome, we searched for genes capable of restoring growth of a TIM-deficient bacterium under gluconeogenic conditions. Rather than discovering an isomerase, we selected yghZ, a gene encoding a member of the aldo-keto reductase superfamily. Here we show that YghZ catalyzes the stereospecific, NADPH-dependent reduction of l-glyceraldehyde 3-phosphate, the enantiomer of the TIM substrate. This transformation provides an alternate pathway to the formation of dihydroxyacetone phosphate.

Mirroring perfection: the structure of methylglyoxal synthase complexed with the competitive inhibitor 2-phosphoglycolate

The crystal structure of the transition-state analogue 2-phosphoglycolate (2PG) bound to methylglyoxal synthase (MGS) is presented at a resolution of 2.0 A. This structure is very similar to the previously determined structure of MGS complexed to formate and phosphate. Since 2PG is a competitive inhibitor of both MGS and triosephosphate isomerase (TIM), the carboxylate groups of each bound 2PG from this structure and the structure of 2PG bound to TIM were used to align and compare the active sites despite differences in their protein folds. The distances between the functional groups of Asp 71, His 98, His 19, and the carboxylate oxygens of the 2PG molecule in MGS are similar to the corresponding distances between the functional groups of Glu 165, His 95, Lys 13, and the carboxylate oxygens of the 2PG molecule in TIM. However, these spatial relationships are enantiomorphic to each other. Consistent with the known stereochemical data, the catalytic base Asp 71 is positioned on the opposite face of the 2PG-carboxylate plane as Glu 165 of TIM. Both His 98 of MGS and His 95 of TIM are in the plane of the carboxylate of 2PG, suggesting that these two residues are homologous in function. While His 19 of MGS and Lys 13 of TIM appear on the opposite face of the 2PG carboxylate plane, their relative location to the 2PG molecule is quite different, suggesting that they probably have different functions. Most remarkably, unlike the coplanar structure found in the 2PG molecule bound to TIM, the torsion angle around the C1-C2 bond of 2PG bound to MGS brings the phosphoryl moiety out of the molecule's carboxylate plane, facilitating elimination. Further, the superimposition of this structure with the structure of MGS bound to formate and phosphate suggests a model for the enzyme bound to the first transition state.