Discovery of novel pathways for carbohydrate metabolism

Closing the gap between the increasing availability of complete genome sequences and the discovery of novel enzymes in novel metabolic pathways is a significant challenge. Here, we review recent examples of assignment of in vitro enzymatic activities and in vivo metabolic functions to uncharacterized proteins, with a focus on enzymes and metabolic pathways involved in the catabolism and biosynthesis of monosaccharides and polysaccharides. The most effective approaches are based on analyses of sequence-function space in protein families that provide clues for the predictions of the functions of the uncharacterized enzymes. As summarized in this Opinion, this approach allows the discovery of the catabolism of new molecules, new pathways for common molecules, and new enzymatic chemistries.     

Steroid-induced sexual differentiation of the developing brain: multiple pathways, one goal

Hormone exposure, including testosterone and its metabolite estradiol, induces a myriad of effects during a critical period of brain development that are necessary for brain sexual differentiation. Nuclear volume, neuronal morphology, and astrocyte complexity are examples of the wide range of effects by which testosterone and estradiol can induce permanent changes in the function of neurons for the purpose of reproduction in adulthood. This review will examine the multitude of mechanisms by which steroid hormones induce these permanent changes in brain structure and function. Elucidating how steroids alter brain development sheds light on how individual variation in neuronal phenotype is established during a critical period.     

Robustness of central carbohydrate metabolism in developing maize kernels

The central carbohydrate metabolism provides the precursors for the syntheses of various storage products in seeds. While the underlying biochemical map is well established, little is known about the organization and flexibility of carbohydrate metabolic fluxes in the face of changing biosynthetic demands or other perturbations. This question was addressed in developing kernels of maize (Zea mays L.), a model system for the study of starch and sugar metabolism. ¹³C-labeling experiments were carried out with inbred lines, heterotic hybrids, and starch-deficient mutants that were selected to cover a wide range of performances and kernel phenotypes. In total, 46 labeling experiments were carried out using either [U-¹³C₆]glucose or [U-¹³C₁₂]sucrose and up to three stages of kernel development. Carbohydrate flux distributions were estimated based on glucose isotopologue abundances, which were determined in hydrolysates of starch by using quantitative ¹³C-NMR and GC-MS. Similar labeling patterns in all samples indicated robustness of carbohydrate fluxes in maize endosperm, and fluxes were rather stable in response to glucose or sucrose feeding and during development. A lack of ADP-glucose pyrophosphorylase in the bt2 and sh2 mutants triggered significantly increased hexose cycling. In contrast, other mutations with similar kernel phenotypes had no effect. Thus, the distribution of carbohydrate fluxes is stable and not determined by sink strength in maize kernels.     

Enzymes of carbohydrate metabolism in the developing rice grain

The levels of reducing and nonreducing sugars, starch, soluble protein, and selected enzymes involved in the metabolism of sucrose, glucose-1-P, and glucose nucleotides were assayed in dehulled developing rice grains (Oryza sativa L. line IR1541-76-3) during the first 3 weeks after flowering. The level of reducing sugars in the grain was highest 5 to 6 days after flowering. The level of nonreducing sugars and the rate of starch accumulation were maximum 11 to 12 days after flowering, when the level of soluble protein was also the highest. The activities of bound and free invertase, sucrose-UDP and sucrose-ADP glucosyltransferases, hexokinase, phosphoglucomutase, nucleoside diphosphokinase, and UDP-glucose and ADP-glucose pyrophosphorylases were high throughout starch deposition, and were maximum, except for nucleoside diphosphokinase which did not increase in activity, between 8 and 18 days after flowering. Soluble primed phosphorylase and ADP glucose-α-glucosyltransferase (starch synthetase) were both present during starch accumulation. Phosphorylase activity was at least 2-fold that of soluble starch synthetase but the synthetase followed more closely the rate of starch accumulation in the grain. The activity of starch synthetase bound to the starch granule also increased progressively with increased starch content of the grain.     

Unusual pathways and enzymes of central carbohydrate metabolism in Archaea

Sugar-utilizing hyperthermophilic and halophilic Archaea degrade glucose and glucose polymers to acetate or to CO2 using O2, nitrate, sulfur or sulfate as electron acceptors. Comparative analyses of glycolytic pathways in these organisms indicate a variety of differences from the classical Emden-Meyerhof and Entner-Doudoroff pathways that are operative in Bacteria and Eukarya, respectively. The archaeal pathways are characterized by the presence of numerous novel enzymes and enzyme families that catalyze, for example, the phosphorylation of glucose and of fructose 6-phosphate, the isomerization of glucose 6-phosphate, the cleavage of fructose 1,6-bisphosphate, the oxidation of glyceraldehyde 3-phosphate and the conversion of acetyl-CoA to acetate. Recent major advances in deciphering the complexity of archaeal central carbohydrate metabolism were gained by combination of classical biochemical and genomic-based approaches.     

Effect of formaldehyde on brain carbohydrate metabolism

The use of formaldehyde makes it possible to decrease the speed of the energy metabolism in the brain without any significant pathological chemical changes in the functional state of the cardiovascular system. The given effect of formaldehyde may account for the attenuation of hypoxic and ischemic disturbances.     

Enzymic capacities of purified cauliflower bud plastids for lipid synthesis and carbohydrate metabolism

Isolated cauliflower (Brassica oleracea) bud plastids, purified by isopycnic centrifugation in density gradients of Percoll, were found to be highly intact, to be practically devoid of extraplastidial contaminations, and to retain all the enzymes involved in fatty acid, phosphatidic acid, and monogalactosyldiacylglycerol synthesis. Purified plastids possess all the enzymes needed to convert triose phosphate to starch and vice versa, and are capable of conversion of glycerate 3-phosphate to pyruvate for fatty acid synthesis. They are also capable of oxidation of hexose phosphate and conversion to triose phosphate via the oxidative pentosephosphate pathway. Cauliflower bud plastids prove to be, therefore, biochemically very flexible organelles.     

Enzymes of carbohydrate metabolism in the developing endosperm of maize

A number of enzymes presumably implicated in starch synthesis were assayed at various stages of endosperm development ranging from 8 days to 28 days after pollination. Activity for invertase, hexokinase, the glucose phosphate isomerases, the phosphoglucomutases, phosphorylase I, uridine diphosphate glucose pyrophosphorylase, and the starch granule-bound nucleoside diphosphate glucose-starch glucosyltransferase was present at the earliest stage of development (8 days) studied. Activity was detectable for phosphorylase III, the soluble adenosine diphosphate glucose-starch glucosyltransferase, adenosine diphosphate glucose pyrophosphorylase, and sucrose-uridine diphosphate glucosyltransferase at 12 days. For phosphorylase II and cytidine diphosphate glucose pyrophosphorylase, activity was first detectable at the 14- and 16-day stages, respectively. Rapid increases in starch content are observed prior to detectable activity for adenosine diphosphate glucose pyrophosphorylase, the soluble adenosine diphosphate glucose-starch glucosyltransferase and phosphorylases II and III. For all enzymes, except invertase, activity per endosperm rises to a peak at 22 or 28 days. Greatest activity for invertase is found at 12 days with a steady decline thereafter. The pattern of invertase activity in comparison with that of sucrose-uridine diphosphate glucosyltransferase supports previous suggestions, that the latter plays a key role in the conversion of sucrose to starch. In addition to phosphorylases I, II, and III, multiple forms of glucosephosphate isomerase and phosphoglucomutase were detected.     

Glycoprotein metabolism in developing mouse brain

—Incorporation of [¹⁴C]fucose or [¹⁴C]glucosamine into the glycoproteins of developing mouse brain was studied using polyacrylamide gel electrophoresis. Between 1 and 10 days after birth two fractions of soluble glycoproteins were extensively labelled, but by 15 days after birth incorporation into these fractions was no longer prominent. These glycoproteins have apparent molecular weights in the range of 150,000-250,000, as estimated by the electrophoretic procedure. The more rapidly migrating fraction has a half-life of about 1 week whereas the other is far more stable.     

Enzymes of carbohydrate metabolism in developing Hordeum distichum grain

Variations in activity of several enzymes associated with carbohydrate metabolism were recorded during the development of barley endosperm. The enzymes investigated were: sucrose-UDP (ADP) glucosyl transferase; invertase; UDPG (ADPG) pyrophosphorylase; hexokinase; glucose-6-phosphate ketoisomerase; phosphoglucomutase, and nucleosidediphosphokinase.     

Enzymes of carbohydrate metabolism in developing grains of high lysine barley mutant

Activities of UDP(ADP)-sucrose synthetase, hexokinase, phosphoglucoisomerase and phosphoglucomutase have been studied in both a high lysine mutant barley, Notch-2 and its parent NP 113 during development. The Notch-2 mutant had higher average activities of UDP(ADP)-sucrose synthetase, hexokinase and phosphoglucomutase and lower activity on a grain basis of phosphoglucoisomerase than NP 113. This reflected the decreased dry matter in the mutant grain. In general, the average activities of hexokinase and phosphoglucomutase per grain did not differ significantly between Notch-2 and NP 113. It is suggested that the lower level of phosphoglucoisomerase in Notch-2 compared with NP 113 would limit the synthesis of glucose 6-phosphate, which in turn would result in reduced starch synthesis.     

Enzymic degradation of allantoate in developing soybeans

A Mn²⁺-dependent enzymic breakdown of allantoate has been detected in crude and partially purified extracts of developing soybeans. The products detected were CO₂, NH₃, glyoxylate, labile glyoxylate derivatives, and low levels of urea. Urea is initially produced at less than 10% the rate of urease-independent CO₂ release indicating that the activity is not allantoate amidinohydrolase (i.e. urea is not directly cleaved off allantoate). The urease-independent CO₂ releasing activity has an apparent K_m of 1.0 millimolar for allantoate. Ethylenediaminetetraacetate, borate, and acetohydroxamate (all at 10 millimolar) inhibit the enzymic production of NH₃, CO₂, and labile glyoxylate derivatives from allantoate. However, the potent urease inhibitor, phenyl phosphordiamidate does not inhibit CO₂ and NH₃ release indicating that the action of acetohydroxamate is not due to its inhibition of urease. That the allantoatedegrading activity was more than 5-fold greater in seed coats than in embryos is consistent with the data of Rainbird et al. (Plant Physiol 1984 74: 329-334) which indicate that available ureides are metabolized before reaching the embryo. 2-Ethanolthio, 2′ureido, acetic acid (NH₂COHNCHCO₂HSCH₂CH₂OH), the first allantoate-derived product detected by HPLC analysis, is an addition produced of mercaptoethanol with an unidentified enzymically produced ureido intermediate that is not derived from ureidoglycolate or oxalurate.     

Enzymic activities of carbohydrate,purine, and pyrimidine metabolism in the Anaeroplasmataceae (class Mollicutes)

Cell-free extracts of two strictly anaerobic mollicutes, Anaeroplasma intermedium 5LA and Asteroleplasma anaerobium 161^T, were tested for enzymic activities of intracellular carbohydrate metabolism. Asteroleplasma anaerobium was also tested for enzymes of purine and pyrimidine metabolism. Both organisms had enzymic activities associated with the nonoxidative portion of the pentose phosphate pathway, and with the Embden-Meyerhoff-Parnas pathway. The 6-phosphofructokinase (PFK) of Asteroleplasma anaerobium was ATP-dependent, whereas the PFK of Anaeroplasma intermedium was PP_i-dependent. The two anaerobic mollicutes also differed with respect to the enzymes that converted phosphoenolpyruvate (PEP) to pyruvate; Anaeroplasma intermedium had pyruvate kinase activity, but Asteroleplasma anaerobium had pyruvate, orthophosphate dikinase activity (PP_i-dependent). Both organisms had lactate dehydrogenase activity which was activated by fructose 1,6-bisphosphate (Fru-1,6-P ₂). Anaeroplasma intermedium had activity for PEP carboxykinase (activated by Fru-1,6-P ₂), but Asteroleplasma anaerobium did not. PEP carboxytransphosphorylase activity was not detected in either organism. Anaeroplasma intermedium had malate dehydrogenase and isocitrate dehydrogenase activities, but it had no activities for the three other tricarboxylic acid cycle enzymes examined; Asteroleplasma anaerobium had malate dehydrogenase activity only. Asteroleplasma anaerobium had enzymic activities for the interconversion of purine nucleobases, (deoxy)ribonucleosides, and (deoxy)ribomononucleotides, including PP_i-dependent nucleoside kinase, reported heretofore only in some other mollicutes. Asteroleplasma anaerobium could synthesize dTDP by the thymine salvage pathway if deoxyribose 1-phosphate was provided, and it had dUTPase, ATPase, and dCMP kinase activities. It lacked (deoxy)cytidine deaminase, dCMP deaminase, and deoxycytidine kinase activities.Abbreviations EMP Embden-Meyerhof-Parnas - ICDH isocitrate dehydrogenase - LDH lactate dehydrogenase - PEP phosphoenolpyruvate - PFK phosphofructokinase - PPDK pyruvate, orthophosphate dikinase - TCA cycle tricarboxylic acid cycle Note: Other abbreviations used are as per the instruction to authors, or the reference cited therein (Eur J Biochem 1:259), or Biochem J 120:449 (which supercedes a portion of the first reference)