The anaplerotic pyruvate carboxylase from white shrimp Litopenaeus vannamei: Gene structure, molecular characterization, protein modelling and expression during hypoxia.

Hypoxic zones are spreading worldwide in marine environments affecting many organisms. Shrimp and other marine crustaceans can withstand environmental hypoxia using several strategies, including the regulation of energy producing metabolic pathways. Pyruvate carboxylase (PC) catalyzes the first reaction of gluconeogenesis to produce oxaloacetate from pyruvate. In mammals, PC also participates in lipogenesis, insulin secretion and other processes, but this enzyme has been scarcely studied in marine invertebrates. In this work, we characterized the gene encoding PC in the white shrimp Litopenaeus vannamei, modelled the protein structure and evaluated its gene expression in hepatopancreas during hypoxia, as well as glucose and lactate concentrations. The PC gene codes for a mitochondrial protein and has 21 coding exons and 4 non-coding exons that generate three transcript variants with differences only in the 5'-UTR. Total PC expression is more abundant in hepatopancreas compared to gills or muscle, indicating tissue-specific expression. Under hypoxic conditions of 1.53 mg/L dissolved oxygen, PC expression is maintained in hepatopancreas, indicating its key role even in energy-limited conditions. Finally, both glucose and lactate concentrations were maintained under hypoxia for 24-48 h in hepatopancreas.

The phosphoenolpyruvate-pyruvate-oxaloacetate node genes and enzymes in Streptomyces coelicolor M-145.

The phosphoenolpyruvate-pyruvate-oxaloacetate node is a major branch within the central carbon metabolism and acts as a connection point between glycolysis, gluconeogenesis, and the TCA cycle. Phosphoenolpyruvate carboxylase, pyruvate carboxylase, phosphoenolpyruvate carboxykinase, malic enzymes, and pyruvate kinase, among others, are enzymes included in this node. We determined the mRNA levels and specific activity profiles of some of these genes and enzymes in Streptomyces coelicolor M-145. The results obtained in the presence of glucose demonstrated that all genes studied of the phosphoenolpyruvate-pyruvate-oxaloacetate node were expressed, although at different levels, with 10- to 100-fold differences. SCO3127 (phosphoenolpyruvate carboxylase gene) and SCO5261 (NADP+-dependent malic enzyme gene) showed the highest expression in the rapid growth phase, and the mRNA levels corresponding to SCO5896 (phosphoenolpyruvate-utilizing enzyme gene), and SCO0546 (pyruvate carboxylase gene) increased 5- to 10-fold towards the stationary phase. In casamino acids, in general mRNA levels of S. coelicolor were lower than in glucose, however, results showed greater mRNA expression of SCO4979 (PEP carboxykinase), SCO0208 (pyruvate phosphate dikinase gene), and SCO5261 (NADP+-dependent malic enzyme). These results suggest that PEP carboxylase (SCO3127) is an important enzyme during glucose catabolism and oxaloacetate replenishment. On the other hand, phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase, and NADP+-malic enzyme could have an important role in gluconeogenesis in S. coelicolor.

Effect of sorghum grain supplementation on glucose metabolism in cattle and sheep fed temperate pasture.

The aim of this work was to evaluate the effect of sorghum grain supplementation on plasma glucose, insulin and glucagon concentrations, and hepatic mRNA concentrations of insulin receptor (INSR), pyruvate carboxylase (PC), and phosphoenolpyruvate carboxykinase (PCK1) mRNA and their association with nutrient intake, digestion and rumen volatile fatty acids (VFA) in cattle and sheep fed a fresh temperate pasture. Twelve Hereford × Aberdeen Angus heifers and 12 Corriedale × Milchschaf wethers in positive energy balance were assigned within each species to one of two treatments (n = 6 per treatment within specie): non-supplemented or supplemented with sorghum grain at 15 g/kg of their body weight (BW). Supplemented cattle had greater plasma glucose concentrations, decreased plasma glucagon concentrations and tended to have greater plasma insulin and insulin-to-glucagon ratio than non-supplemented ones. Hepatic expression of INSR and PC mRNA did not differ between treatments but PCK1 mRNA was less in supplemented than non-supplemented cattle. Supplemented sheep tended to have greater plasma glucagon concentrations than non-supplemented ones. Plasma glucose, insulin, insulin-to-glucagon ratio, and hepatic expression of INSR and PC mRNA did not differ between treatments, but PCK1 mRNA was less in supplemented than non-supplemented sheep. The inclusion of sorghum grain in the diet decreased PCK1 mRNA but did not affect PC mRNA in both species; these effects were associated with changes in glucose and endocrine profiles in cattle but not in sheep. Results would suggest that sorghum grain supplementation of animals in positive energy balance (cattle and sheep) fed a fresh temperate pasture would modify hepatic metabolism to prioritize the use of propionate as a gluconeogenic precursor.

The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential.

BACKGROUND: Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these pathways with sufficient robustness and high yield. In this work we analyzed the genome of the propionic acid producer Actinobacteria Propionibacterium acidipropionici (ATCC 4875). RESULTS: The assembled P. acidipropionici genome has 3,656,170 base pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We identified 3,336 protein coding genes, approximately 1000 more than P. freudenreichii and P. acnes, with an increase in the number of genes putatively involved in maintenance of genome integrity, as well as the presence of an invertase and genes putatively involved in carbon catabolite repression. In addition, we made an experimental confirmation of the ability of P. acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene was found in the genome. Instead, we identified the pyruvate carboxylase gene and confirmed the presence of the corresponding enzyme in proteome analysis as a potential candidate for this activity. Similarly, the phosphate acetyltransferase and acetate kinase genes, which are considered responsible for acetate formation, were not present in the genome. In P. acidipropionici, a similar function seems to be performed by an ADP forming acetate-CoA ligase gene and its corresponding enzyme was confirmed in the proteome analysis. CONCLUSIONS: Our data shows that P. acidipropionici has several of the desired features that are required to become a platform for the production of chemical commodities: multiple pathways for efficient feedstock utilization, ability to fix CO2, robustness, and efficient production of propionic acid, a potential precursor for valuable 3-carbon compounds.

Anaplerotic function of phosphoenolpyruvate carboxylase in Bradyrhizobium japonicum USDA110.

In bacteria, anaplerotic carbon fixation necessary for growth on carbon sources that are metabolized to three-carbon intermediates is provided by the activity of pyruvate carboxylase (PYC) and/or phosphoenolpyruvate carboxylase (PPC). In contrast to other rhizobia, which encode only one of these enzymes in their genomes, Bradyrhizobium japonicum USDA110 encodes both. Streptavidin-HRP western blot analysis of B. japonicum extracts demonstrated the presence of a biotin-containing protein whose molecular mass was indistinguishable from those of PYCs produced by Sinorhizobium meliloti and Rhizobium etli. Sequence analysis of the possible B. japonicum PYC revealed the lack of a pyruvate binding site as well as other characteristics indicating that the enzyme is non-functional, and PPC activity, but not PYC activity, was detectible in extracts prepared from strain USDA110. A B. japonicum cosmid genomic library was used to clone the ppc by functional complementation of S. meliloti pyc mutant RmF991. S. meliloti RmF991-carrying plasmids containing the B. japonicum ppc regained the ability to grow with glucose as a carbon source and produced PPC activity. The cloned ppc gene was inactivated by insertion mutagenesis and recombined into the USDA110 genome. The resulting ppc mutant was essentially devoid of PPC activity and grew poorly with glucose as carbon source in comparison to the wild-type strain. These data indicate that B. japonicum utilizes PPC, and not PYC, as an anaplerotic enzyme for growth on carbon sources metabolized to three-carbon intermediates.

Coupling kinetic expressions and metabolic networks for predicting wine fermentations.

Problematic fermentations are commonplace and cause wine industry producers substantial economic losses through wasted tank capacity and low value final products. Being able to predict such fermentations would enable enologists to take preventive actions. In this study we modeled sugar uptake kinetics and coupled them to a previously developed stoichiometric model, which describes the anaerobic metabolism of Saccharomyces cerevisiae. The resulting model was used to predict normal and slow fermentations under winemaking conditions. The effects of fermentation temperature and initial nitrogen concentration were modeled through an efficiency factor incorporated into the sugar uptake expressions. The model required few initial parameters to successfully reproduce glucose, fructose, and ethanol profiles of laboratory and industrial fermentations. Glycerol and biomass profiles were successfully predicted in nitrogen rich cultures. The time normal or slow wine fermentations needed to complete the process was predicted accurately, at different temperatures. Simulations with a model representing a genetically modified yeast fermentation, reproduced qualitatively well literature results regarding the formation of minor compounds involved in wine complexity and aroma. Therefore, the model also proves useful to explore the effects of genetic modifications on fermentation profiles.

Inactivation of pycA, encoding pyruvate carboxylase activity, increases poly-beta-hydroxybutyrate accumulation in Azotobacter vinelandii on solid medium.

Strain AJ1678, an Azotobacter vinelandii mutant overproducing the storage polymer poly-beta-hydroxybutyrate (PHB) in solid but not liquid complex medium with sucrose, was isolated after mini-Tn5 mutagenesis of strain UW136. Cloning and nucleotide sequencing of the affected locus led to identification of pycA, encoding a protein with high identity to the biotin carboxylase subunit of pyruvate carboxylase enzyme (PYC). A gene ( pycB) whose product is similar to the biotin-carrying subunit of PYC is present immediately downstream from pycA. An assay of pyruvate carboxylase activity and an avidin-blot analysis confirmed that pycA and pycB encode the two subunits of this enzyme. In many organisms, PYC catalyzes ATP-dependent carboxylation of pyruvate to generate oxaloacetate and is responsible for replenishing oxaloacetate for continued operation of the tricarboxylic acid cycle. We propose that the pycA mutation causes a slow-down in the TCA cycle activity due to a low oxaloacetate concentration, resulting in a higher availability of acetyl-CoA for the synthesis of poly-beta-hydroxybutyrate.

Effect of aniA (carbon flux regulator) and PhaC (poly-beta-hydroxybutyrate synthase) mutations on pyruvate metabolism in Rhizobium etli.

The Rhizobium etli poly-beta-hydroxybutyrate synthase (PhaC) mutant SAM100 grows poorly with pyruvate as the carbon source. The inactivation of aniA, encoding a global carbon flux regulator, in SAM100 restores growth of the resulting double mutant (VEM58) on pyruvate. Pyruvate carboxylase (PYC) activity, pyc gene transcription, and holoenzyme content, which were low in SAM100, were restored in strain VEM58. The genetically engineered overexpression of PYC in SAM100 also allowed its growth on pyruvate. The possible relation between AniA, pyc transcription, and reduced-nucleotide levels is discussed.

Cloning and characterization of the pyruvate carboxylase from Sinorhizobium meliloti Rm1021.

The gene encoding pyruvate carboxylase (pyc) was isolated from a Sinorhizobium meliloti Rm1021 cosmid bank by complementation of a Rhizobium tropici pyc mutant. PYC-negative mutants of S. meliloti Rm1021 were isolated by transposon mutagenesis and were unable to grow with glucose or pyruvate as sole carbon sources, but were symbiotically competent in combination with alfalfa plants. PYC activity assays, pyc::lacZ gene fusion studies and an in vivo biotinylation assay showed that PYC activity in S. meliloti was dependent mainly on biotin availability and not on changes in gene transcription. The subunit and holo-enzyme molecular masses of the S. meliloti PYC indicated that the enzyme was an alpha4 homotetramer. The S. meliloti PYC had a high apparent Ka (0.23 mM) for the allosteric activator acetyl-CoA and was product-inhibited by sub-millimolar concentrations of oxaloacetate. In contrast to other bacterial alpha4-PYCs which have been characterized, the S. meliloti enzyme was not strongly inhibited by L-aspartate.

Differential effects of biotin deficiency and replenishment on rat liver pyruvate and propionyl-CoA carboxylases and on their mRNAs.

Although the role of vitamins as prosthetic groups of enzymes is well known, their participation in the regulation of their genetic expression has been much less explored. We studied the effect of biotin on the genetic expression of rat liver mitochondrial carboxylases: pyruvate carboxylase (PC), propionyl-CoA carboxylase (PCC), and 3-methylcrotonyl-CoA carboxylase (MCC). Rats were made biotin-deficient and were sacrificed after 8 to 10 weeks, when deficiency manifestations began to appear. At this time, hepatic PCC activity was 20% of the control values or lower, and there was an abnormally high urinary excretion of 3-hydroxyisovaleric acid, a marker of biotin deficiency. Biotin was added to deficient primary cultured hepatocytes. It took at least 24 h after the addition of biotin for PCC to achieve control activity and biotinylation levels, whereas PC became active and fully biotinylated in the first hour. The enzyme's mass was assessed in liver homogenates from biotin-deficient rats and incubated with biotin to convert the apocarboxylases into holocarboylases, which were detected by streptavidin blots. The amount of PC was minimally affected by biotin deficiency, whereas that of the alpha subunits of PCC and of MCC decreased substantially in deficient livers, which likely explains the reactivation and rebiotinylation results. The expression of PC and alphaPCC was studied at the mRNA level by Northern blots and RT/PCR; no significant changes were observed in the deficient livers. These results suggest that biotin regulates the expression of the catabolic carboxylases (PCC and MCC), that this regulation occurs after the posttranscriptional level, and that pyruvate carboxylase, a key enzyme for gluconeogenesis, Krebs cycle anaplerosis, and fatty acid synthesis, is spared of this control.

Isolation of the Pichia pastoris PYC1 gene encoding pyruvate carboxylase and identification of a suppressor of the pyc phenotype.

We have cloned and characterized a gene encoding pyruvate carboxylase from the methylotrophic yeast Pichia pastoris. Disruption of this gene produced inability to grow in minimal medium with glucose as carbon source and ammonium as nitrogen source. Growth was possible with aspartate or glutamate as nitrogen source. The gene PpPYC1 expressed from its own promoter was able to rescue the phenotype of Saccharomyces cerevisiae mutants devoid of pyruvate carboxylase. In a P. pastoris strain carrying a disrupted PpPYC1 gene we have isolated spontaneous mutants able to grow in non-permissive conditions. In a mutant strain grown in glucose several enzymes sensitive to catabolite repression were derepressed. The strain also had elevated levels of glutamate dehydrogenase (NAD) both in repressed and derepressed conditions.

Regulation of pyruvate carboxylase in Rhizobium etli.

Pyruvate carboxylase (PYC) is a biotin-dependent enzyme catalyzing the anaplerotic conversion of pyruvate to oxaloacetate in Rhizobium etli strain CE3. A pyc::Tn5 mutant had severely reduced growth, or failed to grow on sugars, three-carbon organic acids or glycerol, consistent with these substrates being metabolized via pyruvate. Transconjugants expressing a pyc::beta-glucuronidase gene fusion had slightly increased apparent pyc transcription during growth on pyruvate as compared to succinate, similar to the modest carbon source dependent changes in PYC activity reported previously. Biotin supplementation of cultures growing on pyruvate dramatically increased PYC activity but not apparent pyc transcription. Bacteroids isolated from bean nodules did not contain detectable PYC activity while apparent pyc transcription occurred at a moderate level.