The effect of feeding with a tryptophan-free amino acid mixture on rat liver magnesium ion-activated deoxyribonucleic acid-dependent ribonucleic acid polymerase

Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm

BACKGROUND

Hepatitis is a type of infectious disease that induces inflammation of the liver without pinpointing a particular pathogen or pathogenesis. Type C hepatitis, as a type of hepatitis, has been reported to induce cirrhosis and hepatocellular carcinoma within a very short amount of time. It is a great threat to human health. Some studies have revealed that trace elements are associated with infection with and immune rejection against hepatitis C virus (HCV). However, the mechanism underlying this phenomenon is still unclear.

METHODS

In this study, we aimed to expand our knowledge of this phenomenon by designing a computational method to identify genes that may be related to both HCV and trace element metabolic processes. The searching procedure included three stages. First, a shortest path algorithm was applied to a large network, constructed by protein-protein interactions, to identify potential genes of interest. Second, a permutation test was executed to exclude false discoveries. Finally, some rules based on the betweenness and associations between candidate genes and HCV and trace elements were built to select core genes among the remaining genes.

RESULTS

12 lists of genes, corresponding to 12 types of trace elements, were obtained. These genes are deemed to be associated with HCV infection and trace elements metabolism.

CONCLUSIONS

The analyses indicate that some genes may be related to both HCV and trace element metabolic processes, further confirming the associations between HCV and trace elements. The method was further tested on another set of HCV genes, the results indicate that this method is quite robustness.

GENERAL SIGNIFICANCE

The newly found genes may partially reveal unknown mechanisms between HCV infection and trace element metabolism. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.

A low-protein diet restricts albumin synthesis in nephrotic rats

High-protein diets increase albumin synthesis in rats with Heymann nephritis but albuminuria increases also, causing serum albumin concentration to be suppressed further than in nephrotic animals eating a low-protein diet. Experiments were designed to determine whether dietary protein augmentation directly stimulates albumin synthesis, or whether instead increased albumin synthesis is triggered by the decrease in serum albumin concentration. Evidence is presented that dietary protein augmentation directly stimulates albumin synthesis, accompanied by a proportional increase in steady-state hepatic albumin mRNA concentration (AlbmRNA) and by an increase in AlbmRNA transcription. When the increased albuminuria resulting from dietary protein augmentation is blunted with enalapril, serum albumin concentration is shown to increase in nephrotic rats. Both albumin synthesis and AlbmRNA increase in these animals despite the greater serum albumin concentration. Albumin synthesis correlates inversely with both serum albumin and serum oncotic pressure in nephrotic rats fed 40% protein, but does not correlate with serum albumin concentration in nephrotic rats fed 8.5% protein (LP), even when serum albumin concentration is reduced. Albumin masses are preserved in LP primarily because of reduced albuminuria. Reduced serum oncotic pressure and dietary protein augmentation combine to stimulate albumin synthesis in nephrotic rats at the level of gene transcription.

Albumin metabolism in the nephrotic syndrome: the effect of dietary protein intake

The nephrotic syndrome is characterized by increased urinary excretion of albumin and other serum proteins, accompanied by hypoproteinemia and edema formation. Nephrotic patients have lower serum albumin concentrations than do patients undergoing continuous ambulatory peritoneal dialysis when albumin and protein losses are the same in both groups, suggesting that nephrotic patients may not maximally adapt to loss of protein. The fractional rate of albumin catabolism is increased in nephrotic patients, possibly as a result of increased albumin catabolism by the kidney, but the absolute albumin catabolic rate is decreased in nephrotic patients. The rate of albumin synthesis may be increased, but not sufficiently to maintain normal serum albumin concentration or albumin pools. Augmentation of dietary protein in nephrotic rats directly stimulates albumin synthesis by increasing albumin mRNA content in the liver, but also causes an increase in glomerular permeability to macromolecules so that much if not all of the excess albumin synthesized is lost in the urine. When dietary protein is restricted, the rate of albumin synthesis is not increased either in nephrotic patients or in rats, despite severe hypoalbuminemia. Although dietary protein supplementation may lead to positive nitrogen balance, dietary protein supplementation alone does not cause an increase in serum albumin concentration or body albumin pools, and may instead cause further albumin pool depletion because of changes induced in glomerular permselectivity. The use of angiotensin-converting enzyme inhibitors may blunt the increased albuminuria caused by dietary protein supplementation and allow albumin stores to be increased.

Messenger RNA levels of plasma proteins following fasting

1. The effect of fasting on hepatic mRNA levels of seven plasma proteins was examined in the rat. 2. The levels of mRNA were measured directly in cytoplasmic extracts by hybridization to specific 32P-labelled cDNA probes. 3. Following a 48 h period of fasting, the mRNA levels of apolipoprotein E, apolipoprotein A-IV, albumin, transferrin, and transthyretin decreased by 15-30%, while apolipoprotein A-II decreased by 78% compared with non-fasted control rats. The mRNA for apolipoprotein A-I increased by 33%. 4. These findings suggest that mRNA levels in the liver following fasting are regulated independently and variations in these levels may be due to differences in transcription rates or mRNA stability.

Role of tryptophan in carcinogenesis

This paper reviews some of the earlier experimental studies concerning the role that tryptophan plays in enhancing tumorigenesis induced by selected chemical carcinogens. For many years, tryptophan has been implicated in carcinogenesis of the bladder. The evidence regarding tryptophan's effect on hepatic tumorigenesis is conflicting; an enhancing effect has been reported by some investigators, but a reduction in tumorigenesis has been reported by other workers. Some of the unique effects that tryptophan exerts upon the liver are reviewed. Also, experimental studies from our laboratory are reported in which we observed a potentiating effect of increased dietary tryptophan on the induction of gamma-glutamyltranspeptidase-positive foci in liver when rats were fed a choline-supplemented diet but no potentiation was found when rats were fed a choline-deficient diet for 10 weeks. The results suggest that increased dietary tryptophan has a promoting effect on liver carcinogenesis as measured by the induction of gamma-glutamyltranspeptidase-positive foci in the livers of rats exposed to diethylnitrosamine. The possible significance of these findings is reviewed.

Starvation and hypothyroidism exert an overlapping influence on rat hepatic messenger RNA activity profiles

To assess the effect of starvation and to explore the potential interrelationship of starvation and thyroid status at the pretranslational level, we have analyzed by two-dimensional gel electrophoresis, the hepatic translational products of starved and fed euthyroid and hypothyroid rats. 5 d of starvation resulted in a statistically significant change in 27 of 240 products visualized, whereas hypothyroidism caused a change in 20, both in comparison with the fed euthyroid state. Of considerable interest was that 68% of all changing messenger (m)RNA sequences were common to the hypothyroid and starved groups and showed the same directional shift. Further, both starvation and hypothyroidism yielded comparable decreases in total hepatic cytoplasmic RNA content. Although it has been well established that the level of circulating triiodothyronine (T3) and the level of hepatic nuclear receptors fall in starvation, this reduction cannot account for the observed decrease of total hepatic RNA nor for all of the alterations in the concentrations of specific mRNA sequences. Thus, administration of T3 to starved animals in a dose designed to occupy all nuclear T3 receptors fails to prevent the fall in total RNA and the majority of starvation-induced changes in the level of mRNA sequences. Moreover, starvation of athyreotic animals results in a further decrease in total RNA and in a further change in the level of individual mRNA species. We conclude, therefore, that although the reduced levels of circulating T3 and the nuclear T3 receptors can contribute to the observed results of starvation, the starvation-induced changes are not exclusively mediated by this factor. The striking overlap in the genomic response between hypothyroid and starved animals raises the possibility that those biochemical mechanisms regulated at a pretranslational level by T3 are either not helpful or injurious to the starving animal. The reduction in circulating T3 and nuclear receptor sites together with T3-independent mechanisms initiated in the starved animal may constitute redundant processes designed to conserve energy and substrate in the nutritionally deprived organism.

Tryptophan-induced stimulation of hepatic ornithine decarboxylase activity in the rat

The effect of a single tube feeding of L-tryptophan on hepatic ornithine decarboxylase (ODC) activity in rats was investigated. The levels of ODC activity in the livers of control and experimental rats were assayed in vitro by measuring the release of 14CO2 from DL-[1-14C]ornithine. Single tube feedings of varying levels of L-tryptophan (2.5-30 mg/100 g body wt) to overnight-fasted rats 1 hr before sacrifice exhibited increases in the hepatic ODC activities. L-Tryptophan (30 mg/100 g body wt) tube fed to overnight-fasted rats 1/6 to 12 hr before sacrifice induced hepatic ODC activities which were significantly elevated beginning at 1 hr and peaking at 2 hr (6.5-fold increase over controls). In vitro [14C]leucine incorporation into protein using hepatic microsomes of tryptophan-treated rats was significantly increased at 1 hr in comparison with that of controls. The tryptophan-induced stimulation of hepatic ODC activity was not affected by prior adrenalectomy but was abolished by pretreatment with cycloheximide. These studies demonstrate that a single feeding of L-tryptophan can significantly enhance in the rat the activity of ODC, a key enzyme in the biosynthesis of polyamines.

Cell repair after liver injury: an analysis of some metabolic conditions required for the stimulation of RNA synthesis in postischemic liver nuclei

Nuclei isolated from liver cells recovering from reversible (non-necrogenic) ischemia show an increased RNA synthesis. The postischemic effect is not abolished by previous adrenalectomy and occurs in fasted as well as in fed animals. Treatment with cycloheximide, at a dose that severely inhibits protein synthesis without primary effects on RNA synthesis, suppresses the postischemic stimulation of RNA synthesis even if cycloheximide is administered when stimulation is already well developed. Postischemic liver nuclei respond only weakly to the additional stimulation of RNA synthesis caused by the presence of cytosol and albumin in the incubation medium.

L-Tryptophan action on hepatic RNA synthesis and enzyme induction

L-Tryptophan increases the activity of hepatic amino acid metabolizing enzymes, affects gluconeogenesis and displays a modulatory effect on several enzymes connected with RNA synthesis. The underlying mechanism differ in individual cases and result in both an increase of enzyme synthesis de novo and a decrease of enzyme degradation. Tryptophan displays a unique effect causing aggregation of hepatic polyribosomes connected with enhanced protein synthesis and preceded by a higher transport of poly (A) messenger RNA from the nucleus to the cytoplasm. The variety of rather specific effects mediated by tryptophan brings to mind hormonal action and the existence of specific tryptophan receptors is predicted.

Effects of fasting and tryptophan force-feeding on the activity of hepatic nuclear RNA polymerases in rats

The effects of fasting, and subsequent force-feeding of L-tryptophan on the activity of hepatic nuclear DNA-dependent RNA polymerases were studied in adult (5-6 weeks old), and old (5-6 months) male Wistar rats. Liver nuclei, nucleoli, and nucleoplasmic fraction were isolated from rats following a single tube-feeding of tryptophan or water, and were assayed in vitro for the activity of different RNA polymerases. Whereas in adult rats 24 h of fasting caused a significant reduction in the activity of RNA polymerase I and II, in old rats the activity of only polymerase II was decreased after 24 h of fasting. In fasted adult rats administration of tryptophan promptly restored the activities of both polymerases to the respective normal fed levels, while in old rats none of the polymerases were affected by tryptophan. In fasted adult rats the pattern of response for both forms of polymerases to a single tube-feeding of tryptophan, over a period of 5 h, was found to be biphasic. When ribonuclease activity of nuclei was suppressed by performing incubations at low temperatures (17-30 degrees C) the difference between the two groups for polymerase I was greatly reduced, and for polymerase II the difference was fully abolished. Pre-treatment of fasted adult rats with cycloheximide (1.5 mg/kg) was found to abolish the 30 min tryptophan-mediated stimulation of both polymerase I and II activities. In cycloheximide pretreated rats the activity of polymerase II, but not polymerase I returned to its original level 5 h after tryptophan force-feeding.

Effect of tryptophan on hepatic nuclear free and engaged RNA-polymerases in young and adult rats

Whereas in young rats (2 weeks old), administration of typtophan produced marked enhancement in the activity of both engaged and free polymerases of nuclei, in adult rats (10 weeks old) only the engaged polymerases showed higher activities following tryptophan force-feeding.

Effect of undernutrition on cell generation in the adult rat brain

Cell proliferation and cell death in the lateral ventricular subependymal layer were studied in acutely food-deprived and chronically undernourished 6-week-old rats. The length of the cell cycle was increased by 40-75%, while the DNA synthesis phase of the cycle was prolonged by 70-85%. The rate of cell acquisition was reduced to approximately half the control level, and the proportion of degenerating cells was significantly increased. The response to undernutrition of proliferating cells in the subependymal layer of adult rats differs from that in animals in the first two weeks of life, and resembles that seen in other tissues.

The effect of tryptrophan on nucleocytoplasmic translocation of RNA in rat liver

The effect of the administration of tryptophan on the transport of nuclear poly (A)-containing mRNA to the cytoplasm in rat liver was investigated. Administration of tryptophan to fasted rats pretreated with cordycepin and actinomycin D led to decreased levels of nuclear poly (A)-mRNA and a concomitant increase in the levels of polyribosomal poly (A)-mRNA in the cytoplasm as determined by measuring in vivo incorporation of labeled precursors into hepatic RNA. Using isolated hepatic nuclei of rats prelabeled in vivo with [14C]orotic acid, there was greater release of labeled poly(A)-mRNA into the incubation medium from nuclei of tryptophan-treated rats than from nuclei of control animals. The increased release of RNA from hepatic nuclei of tryptophan-treated animals was not related to the cell sap present in the media since cell saps from livers of control and experimental rats gave similar results. These results support earlier findings which suggest that in the rat tryptophan increases the rate of translocation of hepatic poly(A)-mRNA from nucleus to cytoplasm.

Premature induction of hepatic tryptophan oxygenase

Subcutaneous administration of hydrocortisone acetate to the newborn rat produces a premature induction of hepatic tryptophan oxygenase consisting of a transient rise in activity 6-8 h after treatment, followed by a second sustained rise beginning 40 h later, which plateaus at 10 days of age. Cycloheximide treatment at the midpoint of this second elevation inhibits protein synthesis, but not tryptophan oxygenase activity. In older animals, cycloheximide treatment does both. Tryptophan administration at this midpoint rapidly elevates tryptophan oxygenase activity. This elevation can be partially blocked by treatment with actinomycin D within 1 h of tryptophan administration, but not thereafter. Actinomycin treatment is ineffective in blocking the tryptophan-induced rise in older animals. Administration of hydrocortisone acetate to 5- and 10-day-old pups leads to a more rapid and sustained rise in tryptophan oxygenase activity without appearance of a transient induction phase. Neither tryptophan alone, δ-aminolevulinic acid alone, nor tryptophan plus δ-aminolevulinic acid prematurely induces tryptophan oxygenase in newborn or 5-day-old rats.

Influence of tryptophan on the level of hepatic microsomal cytochrome P-450 in well-fed normal, adrenalectomized, and phenobarbital-treated rats

In well-fed normal male rats, either force-feeding of tryptophan or a single injection of phenobarbital produced significant increments in hepatic microsomal cytochrome P-450 and the associated aniline hydroxylase activity. Administration of both tryptophan and phenobarbital together resulted in even greater stimulation than when the compounds were given alone. Adrenalectomy lowered instead the cytochrome P-450 concentration in comparison with that of normal rats, and administration of tryptophan and phenobarbital in this condition produced no significant increment in cytochrome P-450 concentration. In addition, phenobarbital administered either singly or in combination with tryptophan resulted in 80% mortality, which was reduced to zero by pretreatment with cortisol. While in cortisol-treated adrenalectomized rats administration of phenobarbital caused a 56% increment in cytochrome P-450 as compared to controls, tryptophan produced only a minor (9%) increase. In normal, as well as in adrenalectomized rats, tryptophan and phenobarbital administered either idividually or together increased microsomal protein concentration. In normal rats actinomycin-D treatment reduced both cytochrome P-450 and microsomal protein concentrations below that of the non-treated control levels. Further administration of either tryptophan or phenobarbital slightly increased the level of cytochrome P-450, and the two compounds together caused 40 and 21% increments of the same compared to actinomycin-treated and non-treated controls, respectively.

Nutritional disturbances of protein metabolism in the liver

Nutritional disturbances of protein metabolism in the liver are reviewed in relation to feeding experimental animals the following diets: a) purified diets deficient in amino acids; b) amino acid mixtures or single amino acids; c) protein-free (amino acid-free) diets; or d) hypertonic or hypotonic solutions. The effects of tube-feeding the diets or dietary components for days, hours, or minutes on hepatic polyribosomes and protein synthesis are described. Force-feeding a purified diet free of single essential amino acids induces within days morphologic changes resembling those that occur in humans with kwashiorkor, a world-wide nutritional deficiency disease in children. In this kwashiorkor-like model, hepatic protein synthesis and polyribosomal aggregation are increased. Administration of a complete amino acid mixture or tryptophan alone, but no other single amino acid, produces a rapid stimulation (within minutes) of hepatic protein synthesis and polyribosomal aggregation in animals that had been fasted, fed, or treated with hepatotoxic agents. A single tube-feeding of a protein-free (amino acid-free) diet induces within hours an increase in hepatic protein synthesis in fasted animals. Administration of hypertonic solutions rapidly (within minutes) inhibits, while administration of hypotonic solutions rapidly increases, hepatic protein systhesis. These experimental findings are reviewed in terms of how alterations in regulatory controls of hepatic protein synthesis may be influenced by nutritional disturbances. Such information may be of importance in designing and utilizing nutritional approaches in the therapy of liver diseases.

Response of poly(adenylic acid) polymerase in rat liver nuclei and mitochondria to stravation and re-feeding with amino acids

Poly(adenylic acid) polymerase was extracted from liver nuclei and mitochondria of rats either fed ad libitum, starved overnight or starved and then re-fed with a complete amino acid mixture for 1-3 h. The enzymes were partially purified and assayed by using exogenous primers. Starvation resulted in an 80% decrease in the total activity of the purified nuclear enzyme, and the mitochondrial enzyme activity diminished to almost zero after overnight starvation. Measurements of the protein content of whole nuclei or mitochondria and of the enzyme extracts from these organelles indicated that the decrease in enzyme activity on starvation was not caused by incomplete extraction of the enzyme from the starved animals. Re-feeding the animals with the complete amino acid mixture increased the total activity of poly(A) polymerase from the nuclei and mitochondria by 1.9-fold and 63-fold respectively. Under these conditions, the total protein content of the nuclei and mitochondria increased by only 13 and 32% respectively. These data indicate that poly(A) polymerase is one of the cellular proteins specifically regulated by amino acid supply.

Nucleolar RNA synthesis in the liver of partially hepatectomized and cortisol-treated rats

RNA synthesis by isolated nucleoli from rat liver is significantly enhanced 12--14 h after partial hepatectomy and 4 h after cortisol administration. The increased RNA synthetic capactiy is demonstrable also in the respective high salt nucleolar extracts and in Biogel A-1.5 filtration fractions of the nucleolar extracts. DNA saturation experiments using nucleoli and Biogel fractions from control and treated animals as RNA polymerase source, have demonstrated, that independent of the extent of RNA synthesis, saturation of transcription is reached at the same concentration of exogenous template. We conclude that the activity and not the amount of nucleolar RNA polymerase is increased as a result of partial hepatectomy or cortisol administration. Parallel to the effects on RNA polymerase, the activity, of RNA-degrading enzymes present in nucleoli is also enhanced by the same treatment.

Methylation of newly synthesized ribonucleic acid by isolated rat liver nuclei. Characterization of the ribonucleic acid synthesized by nuclei from starved animals

1. Nuclei from rat liver incubated with S-adenosyl[methyl-(14)C]methionine incorporated radioactivity into RNA and into lipid and protein. 2. All of the labelled RNA was extracted from the nuclei with trichloroacetic acid at 90 degrees C. 3. The [(14)C]methyl-group incorporation into the hot-trichloroacetic acid extract was 30% inhibited by the addition of actinomycin D (100mug/mg of DNA) or by the omission of CTP, GTP and UTP. 4. Assuming that the main substrate for this triphosphate-dependent methylation was newly synthesized precursor rRNA containing one methyl group/30 uridylate residues, it was calculated that approx. 60% of the [(14)C]UMP incorporated under similar conditions represented precursor rRNA synthesis. 5. In agreement with this, low concentrations of actinomycin D (approx. 1mug/mg of DNA) sufficient to abolish the triphosphate-dependent incorporation of [(14)C]methyl group inhibited 68% of the [(14)C]UMP incorporation. 6. The incorporation of [(14)C]UMP by nuclei from starved animals decreased progressively with increasing periods of starvation, whereas the triphosphate-dependent [(14)C]methyl-group incorporation was not further decreased after 1 day of starvation. 7. This suggests that precursor rRNA synthesis decreased within 1 day whereas other species of RNA were affected only after longer periods of starvation.