Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli

The multifunctional proline utilization A (PutA) flavoenzyme from Escherichia coli performs the oxidation of proline to glutamate in two catalytic steps using separate proline dehydrogenase (PRODH) and Δ¹-pyrroline-5-carboxylate (P5C) dehydrogenase domains. In the first reaction, the oxidation of proline is coupled to the reduction of ubiquinone (CoQ) by the PRODH domain, which has a β₈α₈-barrel structure that is conserved in bacterial and eukaryotic PRODH enzymes. The structural requirements of the benzoquinone moiety were examined by steady-state kinetics using CoQ analogs. PutA displayed activity with all the analogs tested; the highest k_cat/K_m was obtained with CoQ₂. The kinetic mechanism of the PRODH reaction was investigated use a variety of steady-state approaches. Initial velocity patterns measured using proline and CoQ₁, combined with dead-end and product inhibition studies, suggested a two-site ping-pong mechanism for PutA. The kinetic parameters for PutA were not strongly influenced by solvent viscosity suggesting that diffusive steps do not significantly limit the overall reaction rate. In summary, the kinetic data reported here, along with analysis of the crystal structure data for the PRODH domain, suggest that the proline:ubiquinone oxidoreductase reaction of PutA occurs via a rapid equilibrium ping-pong mechanism with proline and ubiquinone binding at two distinct sites.     

Kinetics of the transhydrogenase reaction catalyzed by mitochondrial NADH:ubiquinone oxidoreductase (complex I)

The kinetics of the NADH3'-acetylpyridine adenine dinucleotide (APAD⁺) transhydrogenase reaction (DD-reaction) catalyzed by different preparations of mitochondrial NADH-dehydrogenase (submitochondrial particles (SMP), purified Complex I, and three-subunit fragment of Complex I (FP)) have been studied. Complex I (in SMP or in purified preparation) catalyzes two NADHAPAD⁺ reactions with different rates and nucleotide affinities. Reaction 1 has high affinity to APAD⁺ (K_m = 7 M, for SMP) and low rate (V_m = 0.2 mol/min per mg protein, for SMP) and occurs with formation of a ternary complex. Reaction 2 has much higher rate and considerably lower affinity for oxidized nucleotide (V_m = 1.7 mol/min per mg protein and K_m = 160 M, for SMP). FP catalyzes only reaction 1. ADP-ribose inhibits reaction 1 with mixed type inhibition (competitive with non-competitive) with respect to NADH and APAD⁺. Rhein competes with both substrates. The results suggest that at least two nucleotide-binding sites exist in Complex I.     

Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I)

The increasing availability of sequenced genomes enables the reconstruction of the evolutionary history of large protein complexes. Here, we trace the evolution of NADH:ubiquinone oxidoreductase (Complex I), which has increased in size, by so-called supernumary subunits, from 14 subunits in the bacteria to 30 in the plants and algae, 37 in the fungi and 46 in the mammals. Using a combination of pair-wise and profile-based sequence comparisons at the levels of proteins and the DNA of the sequenced eukaryotic genomes, combined with phylogenetic analyses to establish orthology relationships, we were able to (1) trace the origin of six of the supernumerary subunits to the alpha-proteobacterial ancestor of the mitochondria, (2) detect previously unidentified homology relations between subunits from fungi and mammals, (3) detect previously unidentified subunits in the genomes of several species and (4) document several cases of gene duplications among supernumerary subunits in the eukaryotes. One of these, a duplication of N7BM (B17.2), is particularly interesting as it has been lost from genomes that have also lost Complex I proteins, making it a candidate for a Complex I interacting protein. A parsimonious reconstruction of eukaryotic Complex I evolution shows an initial increase in size that predates the separation of plants, fungi and metazoa, followed by a gradual adding and incidental losses of subunits in the various evolutionary lineages. This evolutionary scenario is in contrast to that for Complex I in the prokaryotes, for which the combination of several separate, and previously independently functioning modules into a single complex has been proposed.     

Metabolic engineering of a complex biochemical pathway: The lysine and threonine biosynthesis as an example

The nutritional quality of crop plants is determined by their content in essential amino acids provided in food for humans or in feed for monogastric animals. Amino acid composition of crop–based diets can be improved via manipulation of the properties of key enzymes of amino acid biosynthetic pathways by mutation and transformation. We focused on the aspartate-derived amino acid pathway producing four essential amino acids: lysine, threonine, isoleucine and methionine. Genes encoding aspartate kinase (AK) and dihydrodipicolinate synthase (DHDPS) that operate as key genes of the aspartate pathway have been cloned from Arabidopsis. Genetic and molecular studies revealed that at least five different ak genes are represented. Some of them were characterized in terms of gene and promoter structure, developmental expression and regulatory properties. In the case of dhdps, two quite identical genes have been identified and characterized at expression level. Mutated genes encoding a fully feedback-insensitive form of the DHDPS enzyme were obtained from Nicotiana sylvestris and Arabidopsis. Several chimeric constructs harbouring this mutated allele under the control of constitutive or seed-specific promoters were transferred via Agrobacterium or biolistics in various plant species. In all cases, lines with significant increase of free lysine content were obtained in vegetative organs, but the impact of the transgene in seeds is limited due to the presence of an active catabolic enzyme, lysine ketoreductase. These results show that, although dealing with a complex, highly regulated pathway, the overexpression of a single gene encoding a feedback-insensitive form of the key enzyme DHDPS exerts a significant effect on the carbon flux through the aspartate pathway towards lysine production.     

Binding of the Human “Electron Transferring Flavoprotein” (ETF) to the Medium Chain Acyl-CoA Dehydrogenase (MCAD) Involves an Arginine and Histidine Residue

The interaction between the “electron transferring flavoprotein” (ETF) and medium chain acyl-CoA dehydrogenase (MCAD) enables successful flavin to flavin electron transfer, crucial for the β-oxidation of fatty acids. The exact biochemical determinants for ETF binding to MCAD are unknown. Here we show that binding of human ETF, to MCAD, was inhibited by 2,3-butanedione and diethylpyrocarbonate (DEPC) and reversed by incubation with free arginine and hydroxylamine respectively. Spectral analyses of native ETF vs modified ETF suggested that flavin binding was not affected and that the loss of ETF activity with MCAD involved modification of one ETF arginine residue and one ETF histidine residue respectively. MCAD and octanoyl-CoA protected ETF against inactivation by both 2,3-butanedione and DEPC indicating that the arginine and histidine residues are present in or around the MCAD binding site. Comparison of exposed arginine and histidine residues among different ETF species, however, indicates that arginine residues are highly conserved but that histidine residues are not. These results lead us to conclude that this single arginine residue is essential for the binding of ETF to MCAD, but that the single histidine residue, although involved, is not.     

Biochemical pathways and mechanisms nitrogen, amino acid, and carbon metabolism

For both nitrogen and carbon metabolism there exist specific regulatory mechanisms to enable cells to assimilate a wide variety of nitrogen and carbon sources. Superimposed are regulatory circuits, the so called nitrogen and carbon catabolite regulation, to allow for selective use of “rich” sources first and “poor” sources later. Evidence points to the importance of specific regulatory mechanisms for short term adaptations, while generalized control circuits are used for long term modulation of nitrogen and carbon metabolism. Similarly a variety of regulatory mechanisms operate in amino acid metabolism. Modulation of enzyme activity and modulation of enzyme levels are the outstanding regulatory mechanisms. In prokaryotes, attenuation and repressor/operator control are predominant, besides a so called “metabolic control” which integrates amino acid metabolism into the overall nutritional status of the cells. In eukaryotic cells compartmentation of amino acid metabolites as well as of part of the pathways becomes an additional regulatory factor; pathway specific controls seem to be rare, but a complex regulatory network, the “general control of amino acid biosynthesis”, coordinates the synthesis of enzymes of a number of amino acid biosynthetic pathways.     

调控乳酸菌酸胁迫抗性研究进展

作为工业化的细胞工厂,乳酸菌广泛应用于食品、农业和医药等行业。酸胁迫是乳酸菌在发酵生产以及作为益生菌在人体胃肠道系统中广泛存在的一种环境胁迫,严重影响乳酸菌的生理功能。近年来,随着系统生物学和代谢工程等技术的发展,为进一步揭示乳酸菌酸胁迫抗性机制并提高其耐酸性能带来了可能。本文综述了乳酸菌酸胁迫研究进展,介绍了乳酸菌应对酸胁迫的生理机制,并提出了提升乳酸菌酸胁迫抗性的策略。     

Fermentation in the unicellular cyanobacterium Microcystis PCC7806

The cyanobacterium Microcystis PCC7806 fermented endogenously stored glycogen to ethanol, acetate, CO₂, and H₂ when incubated anaerobically in the dark. The switch from photoautotrophic to fermentative metabolism did not require de novo protein synthesis, and fermentation started immediately after cells had been transferred to dark anoxic conditions. From the molar ratios of the products and from enzyme activities in cell-free extracts, it was concluded that glucose derived from glycogen was degraded via the Embden-Meyerhof-Parnas pathway. In addition, CoA-dependent pyruvate:ferredoxin oxidoreductase, alcohol dehydrogenase, acetate kinase, and hydrogenase were present. The specific activities of these enzymes were sufficiently high to account for the rates of product formation by cell suspensions.     

The effect of acid irrigation on enzyme activities of the single partners of ectomycorrhizas from a limed stand of Norway spruce (Picea abies [L.] Karst.)

The aim of our investigations was to elucidate the effects of acid precipitation on some enzymes of the primary metabolism of ectomycorrhizas. Mycorrhizas of the type of Piceirhiza nigra Gronbach and of Russula ochroleuca (Pers.) Fr. and Tuber puberulum Berk. and Br. were collected from a stand of Norway spruce (Picea abies [L.] Karst.) during the growing seasons of 1991 and 1992. The experimental plots had been limed (Ca: 22 kmol ha_-1, Mg: 20 kmol ha_-1) in 1984 and exposed to acid irrigation (pH 2.7–2.8, H₂SO₄: 2 kmol ha_-1 a_-1) from 1984 to 1990. Crude extracts of mycorrhizas were assayed for the activities of glucose-6-phosphate dehydrogenase (G6P-DH, EC 1.1.1.49), 6-phosphogluconate dehydrogenase (EC 1.1.1.44), NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) and NAD-dependent glutamate dehydrogenase (EC 1.4.1.2). The influence of the experimental treatments on these enzyme activities of the primary metabolism was generally low. For P. nigra, the activity of G6P-DH was decreased on the irrigated plot (photometric determinations). This seems to be a selective effect on the fungal partner, since quantitative enzyme electrophoresis revealed a decrease in the percentage of the fungal enzyme activity in relation to the total enzyme activity, whereas the content of the fungal compound ergosterol was not affected. A decrease in the fungal G6P-DH activity could also be detected in mycorrhizas of Tuber puberulum. There was also a seasonal variation in the proportion of fungal activity of G6P-DH in relation to the total G6P-DH activity. In the photometric assay (total activity) the effect was not discernible. This is indicative of a degree of regulation between the two partners, which could only be detected by quantitative enzyme electrophoresis. In addition, it could be deduced from the electrophoretograms, that in the case of G6P-DH and 6PG-DH the fungal enzyme activity was dominating in all mycorrhizas studied whereas in the case of ICA-DH the fungal band varied from being conspicuous to absent in different species of mycorrhizas. The banding pattern of G6P-DH was reproducibly different for all investigated species of mycorrhizas.