Engineering of Serine-Deamination pathway, Entner-Doudoroff pathway and pyruvate dehydrogenase complex to improve poly(3-hydroxybutyrate) production in Escherichia coli.

BACKGROUND: Poly(3-hydroxybutyrate) (PHB), a biodegradable bio-plastic, is one of the most common homopolymer of polyhydroxyalkanoates (PHAs). PHB is synthesized by a variety of microorganisms as intracellular carbon and energy storage compounds in response to environmental stresses. Bio-based production of PHB from renewable feedstock is a promising and sustainable alternative to the petroleum-based chemical synthesis of plastics. In this study, a novel strategy was applied to improve the PHB biosynthesis from different carbon sources. RESULTS: In this research, we have constructed E. coli strains to produce PHB by engineering the Serine-Deamination (SD) pathway, the Entner-Doudoroff (ED) pathway, and the pyruvate dehydrogenase (PDH) complex. Firstly, co-overexpression of sdaA (encodes L-serine deaminase), L-serine biosynthesis genes and pgk (encodes phosphoglycerate kinase) activated the SD Pathway, and the resulting strain SD02 (pBHR68), harboring the PHB biosynthesis genes from Ralstonia eutropha, produced 4.86 g/L PHB using glucose as the sole carbon source, representing a 2.34-fold increase compared to the reference strain. In addition, activating the ED pathway together with overexpressing the PDH complex further increased the PHB production to 5.54 g/L with content of 81.1% CDW. The intracellular acetyl-CoA concentration and the [NADPH]/[NADP(+)] ratio were enhanced after the modification of SD pathway, ED pathway and the PDH complex. Meanwhile, these engineering strains also had a significant increase in PHB concentration and content when xylose or glycerol was used as carbon source. CONCLUSIONS: Significant levels of PHB biosynthesis from different kinds of carbon sources can be achieved by engineering the Serine-Deamination pathway, Entner-Doudoroff pathway and pyruvate dehydrogenase complex in E. coli JM109 harboring the PHB biosynthesis genes from Ralstonia eutropha. This work demonstrates a novel strategy for improving PHB production in E. coli. The strategy reported here should be useful for the bio-based production of PHB from renewable resources.

Adaptational modification of serine and threonine metabolism in the liver to essential amino acid deficiency in rats.

It is known that plasma serine and threonine concentrations are elevated in rats chronically fed an essential amino acid deficient diet, but the underlying mechanisms including related gene expressions or serine and threonine concentrations in liver remained to be elucidated. We fed rats lysine or valine deficient diet for 4 weeks and examined the mRNA expressions of serine synthesising (3-phosphoglycerate dehydrogenase, PHGDH) and serine/threonine degrading enzymes (serine dehydratase, SDS) in the liver. Dietary deficiency induced marked elevation of hepatic serine and threonine levels associated with enhancement of PHGDH mRNA expression and repression of SDS mRNA expression. Increases in plasma serine and threonine levels due to essential amino acid deficiency in diet were caused by marked increases in hepatic serine and threonine levels. Proteolytic responses to the amino acid deficiency may be lessened by storing amino radicals as serine and inducing anorexia through elevation of threonine.

Mediator requirement downstream of chromatin remodeling during transcriptional activation of CHA1 in yeast.

Mediator complex is essential for transcription by RNA polymerase II in eukaryotes. Although chromatin remodeling is an integral part of transcriptional activation at many promoters, whether Mediator is required for this function has not been determined. Here we have used the yeast CHA1 gene to study the role of Mediator in chromatin remodeling and recruitment of the transcription machinery. We show by chromatin immunoprecipitation that Mediator subunits are recruited to the induced CHA1 promoter. Inactivation of Mediator at 37 degrees C in yeast harboring the srb4-138 (med17) ts mutation severely reduces CHA1 activation and prevents recruitment to the induced CHA1 promoter of Med18/Srb5, from the head module of Mediator, and Med14/Rgr1, which bridges the middle and tail modules. In contrast, recruitment of Med15/Gal11 from the tail module is unaffected in med17 ts yeast at 37 degrees C. Recruitment of TATA-binding protein (TBP) is severely compromised in the absence of functional Mediator, whereas Kin28 and polymerase II recruitment are reduced but to a lesser extent. Induced levels of histone H3K4me3 at the CHA1 promoter are not diminished by inactivation of Mediator, whereas recruitment of Paf1 and of Ser2- and Ser5-phosphorylated forms of Rbp1 are reduced but not eliminated. Loss of histone H3 from the induced CHA1 promoter is seen in wild type yeast but is greatly reduced by loss of intact Mediator. In contrast, Swi/Snf recruitment and nucleosome remodeling are unaffected by loss of Mediator function. Thus, Mediator is required for recruitment of the transcription machinery subsequent to chromatin remodeling during CHA1 induction.

Excess leucine intake induces serine dehydratase in rat liver.

We have hypothesized that rat liver serine dehydratase (SDH) is induced in response to the amount of surplus amino acids from dietary protein. In the present study, we found that excess leucine intake strongly induced SDH activity in the liver but not in the kidney of rats. The increase in activity was accompanied by increases in the levels of SDH mRNA. On the other hand, isoleucine and valine had little effect on SDH induction. These results support our hypothesis and suggest that leucine is a signal for SDH induction.

Serine dehydratase expression decreases in rat livers injured by chronic thioacetamide ingestion.

Serine dehydratase (SerDH) is a gluconeogenic enzyme involved in the catabolism of serine, which is regulated by the composition of their diet and their hormonal status in rats. This study examines how chronic injury caused to the liver of rats by the ingestion of thioacetamide (TAA) affects SerDH protein, mRNA levels, enzyme kinetics and its tissue location. After 97 days' oral intake of TAA, the activity of SerDH at all substrate concentrations assayed was about 60% lower than in controls. No significant differences in Km values were found between the treated group and controls. Immunoblotting and immunohistochemistry revealed a significant reduction in the level of SerDH protein in the livers of the treated rats. SerDH was detected specifically in the periportal zone of the hepatic acinus and this location did not change in response to TAA treatment. The level of SerDH mRNA, quantified by reverse transcription and polymerase chain reaction, was significantly lower in treated rats than in the controls. The present findings suggest that the SerDH expression is rendered to be down regulatory during chronic liver injury induced by TAA. These results enhance our understanding about the biochemical mechanisms implied in the control and integration of serine catabolism during liver injury in rat.

Identification of distinct genes with restricted expression in the somitic mesoderm in Xenopus embryo.

We have used whole-mount in situ hybridisation to identify genes expressed in the somitic mesoderm during Xenopus early development. We report here the analysis of eight genes whose expression pattern has not been described previously. They include the Xenopus homologues of eukaryotic initiation factor 2beta, methionine adenosyltransferase II, serine dehydratase, alpha-adducin, oxoglutarate dehydrogenase, fragile X mental retardation syndrome related protein 1, monocarboxylate transporter and voltage-dependent anion channel 1. Interestingly, these genes exhibit very dynamic expression pattern during early development. At early gastrula stages several genes do not show localised expression pattern, while other genes are expressed in the marginal mesoderm or in ectoderm. As development proceeds, the expression of these genes is gradually restricted to different compartments of somite. This study thus reveals an unexpected dynamic expression pattern for various genes with distinct function in vertebrates.

Postprandial changes in portal venous free amino acids and insulin/glucagon ratios as the result of protein over-intake are not directly linked to serine dehydratase induction in rat liver irrespective of age.

The activity of hepatic serine dehydratase (SDH) increases in tandem with its gene expression when the intake of protein greatly exceeds protein requirements. The actual conditions of plasma free amino acids and pancreatic hormones in weanling and mature rats when fed SDH-inducible and non-inducible diets were examined in relation to incentive factors to secure high SDH activity from a physiological standpoint. Both weanling and mature groups differing in protein requirements were allowed free access to respective diets diverse in protein content (i.e. 25% or 50% casein diet for the former and 6% or 25% casein diet for the latter) during the dark cycle (lights-out) over a period of 1 wk. Despite the difference in protein intake among these groups, there were no conspicuous changes in the plasma concentration of the urea or total or essential amino acids. Therefore, it appears that the individual amino acids did not up regulate the gene and function expressions of SDH merely by their superabundance and subsequent disposal. Portal venous insulin concentration was far higher in mature groups than in weanling groups, although there was little difference between the two groups of the same age in terms of insulin or glucagon concentration and their ratio in abdominal vena cava blood. Accordingly, it follows that the SDH gene undergoes transcriptional regulation through a combined signaling pathway triggered by perceiving surplus protein nutrition as a whole rather than directly through already-known plasma constituents such as free amino acids or pancreatic hormones in the circulatory system.

Response of the induction of rat liver serine dehydratase to changes in the dietary protein requirement.

Growing and mature rats were examined for the effect of a change in dietary protein requirements on the induction of liver serine dehydratase (SDH). The rats were fed on diets varying in casein content, and the weight change and nitrogen balance was determined. SDH activity and its gene expression were induced in both growing and mature rats when their protein intake exceeded their nutritional requirements.

Paracoccus seriniphilus sp. nov., an L-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa.

A novel marine Gram-negative, non-motile, non-spore-forming, aerobic bacterium, associated with the bryozoan Bugula plumosa, was isolated in a screening programme for strains containing enzymes able to convert the amino acid L-serine. Strain MBT-A4T produced L-serine dehydratase and was able to grow on L-serine as the sole carbon and nitrogen source. The nearest phylogenetic neighbour was Paracoccus marcusii, as determined by 16S rDNA sequence analysis (97.8% similarity). The DNA-DNA reassociation value obtained for Paracoccus marcusii DSM11574T and MBT-A4T was 32.6%. The major ubiquinone was 0-10. Based on genotypic, chemotaxonomic and physiological characteristics, a new species of the genus Paracoccus is proposed, Paracoccus seriniphilus sp. nov., the type strain being strain MBT-A4T (=DSM 14827T =CIP 107400T).

Cloning and expression of the two genes coding for L-serine dehydratase from Peptostreptococcus asaccharolyticus: relationship of the iron-sulfur protein to both L-serine dehydratases from Escherichia coli.

The structural genes sdhA and sdhB, coding for the alpha- and beta-subunits of the [4Fe-4S] cluster containing L-serine dehydratase from Peptostreptococcus asaccharolyticus, have been cloned and sequenced. Expression of modified sdhB together with sdhA in Escherichia coli led to overproduction of active His6-tagged L-serine dehydratase. E. coli MEW22, deficient in the L-serine dehydratase L-SD1, was complemented by this sdhBA construct. The derived amino acid sequence of SdhBA shares similarities with both monomeric L-serine dehydratases, L-SD1 and L-SD2, from E. coli and with a putative L-serine dehydratase from Haemophilus influenzae, which suggests that these three enzymes are also iron-sulfur proteins.

Over expression of inducible proteins in Escherichia coli by treatment with ethanol.

It is reported that ethanol enhances DNA synthesis in E. coli cells [Basu, T and Poddar, R. K. (1994), Folia. Microbiol. 39, 3-6]. This communication reports that during growth of E. coli in the presence of 5% v/v ethanol, the derepressed expression of the cytoplasmic enzymes beta-galactosidase and D-serine deaminase per cell increased approximately three fold, while that of the periplasmic enzyme alkaline phosphatase decreased approximately 40% compared to control cell levels. However, in cells transformed with the plasmid pSM 456, bearing phoA-lacZ fusion, the level of induced synthesis of the hybrid protein PhoA-LacZ, controlled by the phoA promoter, was elevated by 25% in the presence of 5% v/v ethanol. This result suggests that the induction of the alkaline phosphatase precursor has also been enhanced by the ethanol treatment, but the inhibition in the export of the precursor across the cytoplasmic membrane, by the influence of ethanol, may represent the reason for the deficient expression of active alkaline phosphatase. It is proposed that there is an ethanol-mediated increase in DNA synthesis, resulting in gene amplification, which may enhance the synthesis of inducible proteins in ethanol-treated cells.

Recovery of mRNA expression of tryptophan 2,3-dioxygenase and serine dehydratase in long-term cultures of primary rat hepatocytes.

Expression of tryptophan 2,3-dioxygenase (TO) and serine dehydratase (SDH) has not previously been maintained or re-induced in long-term cultured hepatocytes. In the present study, we succeeded in inducing expression of TO and SDH mRNAs in adult rat hepatocytes cultured in serum-free L-15 medium supplemented with epidermal growth factor and 2% dimethyl sulfoxide (DMSO). After the start of culture, the expression of TO mRNA rapidly disappeared and at 96 h it was less than 10% of that at isolation. However, after the addition of 2% DMSO from 96 h, the transcript level gradually increased and reached about 40% of that of the isolated cells at day 14. In addition, the expression of TO mRNA was enhanced in cells treated with both 10(-5) M dexamethasone and 10(-7) M glucagon. In contrast, the expression of SDH mRNA decreased very rapidly and we could not detect it after 24 h of culture. Furthermore, 2% DMSO failed to induce it. However, when both 10(-5) M dexamethasone and 10(-7) M glucagon were added to the culture medium at day 9, we observed dramatic induction of SDH mRNA 24 h later. Primary hepatocytes cultured by this method could express and maintain highly differentiated hepatic functions for a long time. Thus, this in vitro system is suitable for the investigation of hepatic functions.

Effects of insulin, epinephrine, and glucose on regulation of transcription of the serine dehydratase gene in newborn dogs.

Our previous investigation showed that hyperinsulinemia incompletely suppressed the transcription of the gene encoding L-serine dehydratase (SDH) (EC 4.2.1.13), a gluconeogenic enzyme, in newborn dogs. To test another hypothesis that insulin resistance in newborn mammals may be partially due to counterregulatory factors, such as epinephrine, euglycemic hyperinsulinemic clamps, hyperglycemic hyperinsulinemic clamps, and hyperglycemic hyperinsulinemic hyperepinephrinemic clamps were performed in newborn dogs in the present study. The infusion rates of insulin and epinephrine were 30 m U/kg/min and 150 ng/kg/min, respectively; the glucose infusion rate was adjustable. The SDH mRNA levels in kidney and liver of newborn dogs were quantitatively analyzed by using rat SDH cDNA probe and by a personal densitometer. The results showed that insulins, glucose, and epinephrine did not change the kidney SDH mRNA level; hyperinsulinemia and hyperglycemia reduced the liver SDH mRNA level by 8.5 and 29.2%, respectively; in the presence of hyperglycemia and hyperinsulinemia, epinephrine was able to increase the liver SDH mRNA by 27.8%, almost offsetting the reduction of the liver SDH mRNA level induced by the combination of insulin and glucose. We conclude that the enhanced regulatory effect of epinephrine counteracting insulin on SDH gene transcription in liver of newborn dogs may be one of the mechanisms responsible for the neonatal insulin resistance which contributes to neonatal hyperglycemia.

Diurnal rhythms of rat liver serine dehydratase, D-site binding protein, and 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA levels are altered by destruction of the suprachiasmatic nucleus of the hypothalamus.

It is generally accepted that a clock generating biological rhythms exists in the suprachiasmatic nuclei (SCN) of the hypothalamus in rodents. We have examined if diurnal variations of rat liver serine dehydratase (SDH), D-site binding protein (DBP), and 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGR) mRNA levels, each of which exhibits low values during the daytime (06:00-18:00) and high values during the dark period, are controlled by the SCN. The SCN were destructed electrolytically, and, 2 weeks later, rats were sacrificed at 06:00, 12:00, 18:00, and 24:00. Completeness of SCN lesions was assessed by the alteration of spontaneous locomotor activity and histological examination of the brains. The SDH and DBP mRNA levels in SCN-lesioned rats were very low at 06:00 and almost eliminated at 18:00, whereas the HMGR mRNA level at 06:00 was low at 06:00 and slightly increased at 18:00 compared to the control values. When determined at 12:00 and 24:00, the SDH, DBP, and HMGR mRNA levels in sham-operated rats were higher at 24:00 than at 12:00, whereas those in SCN-lesioned rats were higher at 12:00 than at 24:00. The hepatic beta-actin and glycine N-methyltransferase mRNA levels showed no significant diurnal variation and were not affected by SCN lesions. These results indicate that the SCN also play a pivotal role in determining rhythmic gene expression in liver.

Periportal expression of the serine dehydratase gene in rat liver.

The mRNA for rat liver serine dehydratase, a gluconeogenic enzyme, exhibits a circadian rhythm with a maximum at the onset of darkness marking the end of the fasting period and a minimum at the onset of light that marks the end of the feeding period, when rats have free access to food and water. In situ hybridization with an antisense cRNA probe revealed that serine dehydratase mRNA was localized in the periportal area of rat liver parenchyma in the evening, whereas it was scarce in the liver in the morning. The predominant localization of serine dehydratase mRNA in the periportal area also occurred in livers of rats that underwent laparotomy, glucagon and dexamethasone administration, and streptozotocin-induced diabetes mellitus, all of which are known to induce serine dehydratase mRNA levels remarkably. Immunostaining revealed that the localization of serine dehydratase protein agreed with that of succinate dehydrogenase, another enzyme known to be predominant in the periportal zone. Thus, the periportal serine dehydratase gene expression strongly supports the idea of metabolic zonation that gluconeogenesis from amino acids occurs preferentially in the periportal parenchyma of rat liver.

Laparotomy causes a transient induction of rat liver serine dehydratase mRNA.

Rat liver serine dehydratase mRNA shows rhythmicity with a high level at the onset of dark (19:00) and a low level at the onset of light (07:00). We have examined the effect of stress (laparotomy) on the rhythm. Upon laparotomy at 09:00 or 17:00, a marked induction of serine dehydratase mRNA occurred 2 h after operation. The elevated mRNA level then decreased and the original mRNA rhythm resumed 2 days later. By contrast, the transcription activator protein DBP mRNA level which shows a similar oscillation was not affected by this treatment. The induction was also seen in adrenalectomized rats that had been treated with hydrocortisone but not with saline or noradrenaline, indicating that glucocorticoids are absolutely necessary for the induction. Pretreatment of rats with phenoxybenzamine, and prazosin prevented the effect of laparotomy, but propranolol and yohimbine had no effect, indicating the necessity of the alpha 1-adrenergic stimulation for the induction. These results suggest that laparotomy releases glucocorticoids and neural noradrenaline that stimulates alpha 1-adrenergic receptors, thereby leading to the serine dehydratase gene expression.

Diurnal variation of the serine dehydratase mRNA level in rat liver.

Serine dehydratase mRNA in the livers of rats maintained on laboratory chow (containing 22% protein) under a 12-h light (7:00-19:00)/12-h dark (19:00-7:00) cycle showed a daily oscillation that was maximal at 19:00 and minimal at 7:00 with an amplitude of more than 20-fold. The feeding of high-protein diets (60 and 91% casein) did not affect the oscillation phase. Virtually identical oscillatory phases for the mature serine dehydratase mRNA and its precursor RNAs, and the results of nuclear run-off transcription assays indicated that the oscillation was generated at the level of transcription. Similar oscillation patters were seen in adrenalectomized, starved, or diabetic rats. However, the mRNA oscillation was not precisely reflected in the oscillation of enzyme activity or enzyme protein in both the phase and the amplitude. Rats maintained on laboratory chow under constant light for 2 weeks still showed mRNA oscillation with a peak at 3:00, whereas rats exposed to constant light and fed between 7:00 and 9:00 exhibited an oscillation peak at 3:00-7:00. Under the conditions of a 12-h light/dark cycle and a 2-h restricted feeding between 7:00 and 9:00, a broad peak was seen at 23:00-3:00. These results indicate that the rhythmic expression of serine dehydratase gene is controlled by both meal-responsive and photoresponsive regulators.

A regulatory element in the CHA1 promoter which confers inducibility by serine and threonine on Saccharomyces cerevisiae genes.

CHA1 of Saccharomyces cerevisiae is the gene for the catabolic L-serine (L-threonine) dehydratase, which is responsible for biodegradation of serine and threonine. We have previously shown that expression of the CHA1 gene is transcriptionally induced by serine and threonine. Northern (RNA) analysis showed that the additional presence of good nitrogen sources affects induction. This may well be due to inducer exclusion. To identify interactions of cis-acting elements with trans activators of the CHA1 promoter, we performed band shift assays of nuclear protein extracts with CHA1 promoter fragments. By this approach, we identified a protein-binding site of the CHA1 promoter. The footprint of this protein contains the ABF1-binding site consensus sequence. This in vitro binding activity is present irrespectively of CHA1 induction. By deletion analysis, two other elements of the CHA1 promoter, UAS1CHA and UAS2CHA, which are needed for induction of the CHA1 gene were identified. Each of the two sequence elements is sufficient to confer serine and threonine induction upon the CYC1 promoter when substituting its upstream activating sequence. Further, in a cha4 mutant strain which is unable to grow with serine or threonine as the sole nitrogen source, the function of UAS1CHA, as well as that of UAS2CHA, is obstructed.

Identification of regions in the rat serine dehydratase gene responsible for regulation by cyclic AMP alone and in the presence of glucocorticoids.

Transcription of the rat serine dehydratase (SDH) gene is induced by glucagon, mediated by the action of cAMP. To identify the nucleotide sequences in the SDH gene responsible for this regulation, we constructed chimeric genes containing different portions of the 5' flanking region of the rat SDH gene fused to the structural sequence encoding the bacterial reporter enzyme, chloramphenicol acetyltransferase (CAT). The transcriptional activities of the fusion genes introduced into the rat hepatoma cell line 7AD-7 were assayed by measuring CAT activity in the cell lysates. Chlorophenylthio-cyclic AMP (CPT-cAMP), a potent protein kinase A activating agent, stimulated the expression of SDH-CAT fusion genes, and these inductions could be enhanced further by the addition of dexamethasone, although the glucocorticoid alone had no effect on CAT activity. Deletion analysis demonstrated that an 80 bp region located approximately 3.5 kb upstream from the transcription initiation site of the rat SDH gene was responsible for stimulation of transcription by CPT-cAMP, whereas the 120 bp region immediately upstream of the cAMP responsive element (CRE)-containing sequences is essential for the enhancement of CPT-cAMP induction by the glucocorticoid.

Location and characterization of multiple glucocorticoid-responsive elements in the rat serine dehydratase gene.

Transcription of the gene coding for serine dehydratase (SDH, EC 4.2.1.13) in the rat in vivo is dramatically increased by glucocorticoid hormones. To identify DNA elements mediating the glucocorticoid-regulated expression of the SDH gene, we transiently transfected 7AD-7 rat hepatoma cells with fusion genes consisting of various regions of the SDH 5' flanking sequence linked to the coding sequence of the gene for chloramphenicol acetyltransferase (CAT). Analysis of the CAT activities from these 5' deletion mutants identified three closely associated glucocorticoid-responsive elements (GREs), located more than 5 kb upstream relative to the cap site. Two distal GREs act synergistically to confer strong glucocorticoid inducibility to the gene, whereas the proximal GRE functions independently of the distal GREs and confers only a weak hormone response to the gene. The purified DNA-binding domain of rat glucocorticoid receptor binds to the sequence of each GRE as shown by footprinting experiments. However, only one of these sequences contains the TGTTCT consensus sequence reportedly associated with many other GREs.