Conservation of ribosomal RNA during compensatory renal hypertrophy. A major mechanism in RNA accretion

Development of a Real-Time TaqMan PCR Method for Absolute Quantification of the Biocontrol Agent Esteya vermicola

Esteya vermicola has been used as an effective biocontrol agent for the management of the pinewood nematode, Bursaphelenchus xylophilus. Tools for monitoring the colonization and parasitism patterns of E. vermicola are required for the development of highly effective biocontrol strategies. Because the TaqMan PCR technique is effective for quantification of species in environmental samples, a real-time PCR-based methodology was developed for absolute quantification of E. vermicola via internal standard addition and extrapolation of DNA quantity to hyphal length. Primers and a probe for the 28S ribosomal RNA gene of E. vermicola were designed, and nested TaqMan real-time PCR-based quantification was performed. In addition, internal standard-based yield measurement was correlated to the absolute quantity of target genomic DNA. Moreover, an extrapolation curve obtained by optical microscopy and image analysis of the mycelia was constructed for the measurement of fungal hyphal length. The absolute quantification method developed in the present study provides a sensitive and accurate technique to quantify fungal density in either wood or other substrate samples and can be used as an effective tool for future studies of biocontrol agents.

Dysregulation of RNA polymerase I transcription during disease

Transcription of the ribosomal RNA genes by the dedicated RNA polymerase I enzyme and subsequent processing of the ribosomal RNA are fundamental control steps in the synthesis of functional ribosomes. Dysregulation of Pol I transcription and ribosome biogenesis is linked to the etiology of a broad range of human diseases. Diseases caused by loss of function mutations in the molecular constituents of the ribosome, or factors intimately associated with RNA polymerase I transcription and processing are collectively termed ribosomopathies. Ribosomopathies are generally rare and treatment options are extremely limited tending to be more palliative than curative. Other more common diseases are associated with profound changes in cellular growth such as cardiac hypertrophy, atrophy or cancer. In contrast to ribosomopathies, altered RNA polymerase I transcriptional activity in these diseases largely results from dysregulated upstream oncogenic pathways or by direct modulation by oncogenes or tumor suppressors at the level of the RNA polymerase I transcription apparatus itself. Ribosomopathies associated with mutations in ribosomal proteins and ribosomal RNA processing or assembly factors have been covered by recent excellent reviews. In contrast, here we review our current knowledge of human diseases specifically associated with dysregulation of RNA polymerase I transcription and its associated regulatory apparatus, including some cases where this dysregulation is directly causative in disease. We will also provide insight into and discussion of possible therapeutic approaches to treat patients with dysregulated RNA polymerase I transcription. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Concentration of phosphoribosyl pyrophosphate in renal hypertrophy. Contrasting effects of early diabetes and unilateral nephrectomy

Studies were made of the renal phosphoribosyl pyrophosphate (PPRibP) content and PPRibP synthetase (EC 2.7.6.1) activity in rats diabetic for 5, 14 or 20 days, or unilaterally nephrectomized (UN) for 5 days, and in doubly lesioned animals. Approximately equal degrees of renal enlargement were found after 5 days diabetes or 5 days UN. In the doubly lesioned animals the increment of growth was additive. Unilateral nephrectomy of 5 days duration, in contrast with diabetes, had no effect on the PPRibP content of the contralateral kidney, nor did it modify the renal PPRibP content when performed on animals diabetic for 5, 14 or 20 days. The activity of PPRibP synthetase was unaffected by diabetes, UN or diabetes +UN. The results pinpoint a stage of nucleotide synthesis which is differentially affected by the two stimuli, in line with evidence for differences in regulation of nucleic acid turnover in the two conditions.

Increased formation and keeping of ribosomes during dietary recovery of mouse kidney

In the kidney of 5-day protein-depleted mice there is a decrease of 23% in the rRNA mass. When these animals are fed with a complete diet, rRNA content is restored to its normal value after 24 h of refeeding. The mechanisms that underlie this phenomenon were studied. It was found that the activity of rRNA polymerase I in the nuclei of kidneys from refed mice showed an increase of about twofold compared with the activity in normal and protein-depleted nuclei. The in vivo incorporation of a large dose (nontrace) of [14C]orotic acid into rRNA was also twofold enhanced in kidneys from refed mice. Ribosome degradation (measured by the disappearance of radioactivity from either ribosomal proteins or rRNA previously labeled by the injection of NaH14CO3 and [14C]orotic acid to the mice, respectively) stopped during the 1st day after refeeding. The estimation of the difference between the rRNA synthesis rate and the net rRNA increase also demonstrated a decrease in the rRNA degradation rate in refed mice.

Re-utilization of pyrimidine nucleotides during rat liver regeneration

The changes in the specific radioactivities of the pool of total acid-soluble uridine nucleotides and of uridine and cytidine components of total cellular and nuclear RNA were monitored in regenerating rat liver for 12 days after partial hepatectomy. Evidence is presented for the re-utilization of pyrimidine nucleotides derived from cytoplasmic RNA degradation for the synthesis of new RNA. The extent of recycling was assessed and the true rate of rRNA turnover determined more accurately. The reutilization of the uridine components of RNA was 7.0%/day during the proliferative and 3.2%/day during the post-proliferative phase, whereas that of the cytidine nucleotides was more pronounced (9.6%/day and 18.1%/day respectively). The results reveal the existence of partial compartmentalization of pyrimidine ribonucleoside triphosphate pools in the nucleus and cytoplasm of rat liver cells.

Kidney function after unilateral nephrectomy

Immediately after unilateral nephrectomy ( uNX ) some different mechanisms of compensatory adaptation begin to act followed by a restoration of sufficient kidney function in a short time period. Beside biochemical changes early compensatory hypertrophy of the remaining kidney occurs. Simultaneously, functional adaptations of renal blood flow, glomerular filtration and exertion of electrolyte and xenobiotics take place. With a suitable pretreatment it is principally possible to accelerate the regeneration phase. Thus the phase of reduced excretion capacity of tubularly secreted xenobiotics after removal of one kidney can be shortened or prevented.

Humoral factors in regulation of compensatory renal hypertrophy

Compensatory renal hypertrophy in transplanted kidneys shows that the major regulators are humoral. Crosscirculation experiments are confirmatory indicating further that the regulators are short-lived and must be consistently present during the early phases of hypertrophy. Controls are difficult to achieve in other systems; variables relate to nutrition, means of assay, pharmacokinetics, and abnormalities produced by the experimental model itself. A simple hypothesis to account for the events precipitating renal hypertrophy might integrate the onsets of renal hyperemia soon after contralateral nephrectomy with the activation of pre-existing stimulators specific for the kidney.

Turnover of ribosomes in regenerating rat liver

The turnover of ribosomes was studied in regenerating liver and the rates of ribosome degradation in the proliferative (1-5 days) and post-proliferative (6-12 days) phases after partial hepatectomy compared: Ribosome turnover during the first 3 days is slower, the half-life of ribosomes being approximately 300 hr. Ribosome synthesis is markedly activated--39% synthesis rate, which corresponds to 34% accumulation rate per day. The half-life of ribosomes during the second phase is about 107 hr. The rate of synthesis falls down to 19% the net gain of ribosomes being 3% per day.

The breakdown of Tetrahymena ribosomes in vivo. The effects of inhibitors

1. When Tetrahymena were deprived of nutrients 50% of the polysomes disaggregated within 20 min and 20% of the total RNA broke down in 2 h. Ribosomal RNA accounted for 75% of the RNA breakdown. 2. RNA labelled by a long incubation with [14C]uridine was stable in growing cells and in the presence of actinomycin D, but broke down at the same rate as bulk RNA in starved cells. 3. The following substances inhibited the loss of RNA during starvation: cycloheximide (which inhibited both polysome disaggregation and protein synthesis), inhibitors of energy metabolism and puromycin (all of which caused polysome disaggregation and inhibited protein synthesis), and chloroquine and 7-amino-1-chloro-3-L-tosylamidoheptan-2-one ('TLCK') (neither of which affected polysomes or protein synthesis). 4. Starvation appears to activate a ribosome degradation mechanism that may involve lysosomal and non-lysosomal enzymes.

Reutilization of preformed pyrimidines for the synthesis of DNA in rat liver and kidney

The specific activities of rat liver and kidney DNA pyrimidines increase in animals which have had [2-14C]-orotic acid administered several days before killing. This phenomenon is caused by the reutilization of the preformed labeled pyrimidine components originating mainly from degraded RNAs of the organism.

Differential effects of folic acid on water content, protein and microsomal 5'-phosphodiesterase activity of the rat kidney

The effects of folic acid administration on the weight, protein, water content and microsomal 5'-phosphodiesterase of the rat kidney were determined, to elucidate the mechanisms contributing to the renal enlargement produced by this agent. Folic acid administered ip in single doses of 100-250 mg/kg caused dose-related increases in kidney weight, water and protein content within 24 hr. Time-course studies indicated that 250 mg folic acid/kg given ip produced a progressive elevation in renal water content from 2 to 72 hr. Smaller increases in whole-kidney protein were recorded 8, 24 and 72 hr after folic acid treatment. However, a biphasic response of microsomal 5'-phosphodiesterase was produced, inhibition at 16 hr being followed by stimulation (to 140% of control) at 72 hr. In vitro studies indicated that folic acid inhibits 5'-phosphodiesterase competitively, and the early inhibition of 5'-phosphodiesterase in vivo appears to be due to a direct effect of folic acid on the enzyme.

Alterations in glomerular RNA in diabetic rats: roles of glucagon and insulin

Incorporation in vivo of labeled orotate into RNA and total nucleotides was measured in isolated glomeruli and whole renal cortex. In 2-day diabetic animals, glomerular RNA was increased, and there was greater incorporation of orotate into total nucleotides and RNA as compared with controls. Insulin reversed the exaggerated incorporation at infusion rates that corrected hyperglucagonemia without reducing plasma glucose and with only minimal changes in insulin concentrations. The addition of glucagon to insulin infusions reproduced the increased incorporation observed in untreated diabetics. Similar changes occurred in renal cortex, where differences in orotate incorporation into nucleotide precursors seemed to be the main cause for alterations in RNA labeling. Isotope incorporation in glomeruli correlated positively with plasma glucagon, but not with insulin or glucose concentrations. Although in 7-month diabetic animals orotate incorporation into RNA was less than in controls, probably as a consequence of renal disease, 24-hour insulin infusion decreased it further. Our results confirm that in the diabetic kidney, abnormal uracil nucleotide metabolism and increased cellular content of RNA are demonstrable in glomeruli as in the renal cortex. These changes appear to be related directly to hyperglucagonemia.

Increased transcription and decreased degradation control and recovery of liver ribosomes after a period of protein starvation

In the livers of 5-days-protein-depleted mice there is a decrease of 47% of the ribosome mass. When these animals are fed with an adequate diet, ribosome content is restored to the normal value after 1 day of re-feeding. The mechanisms underlying this phenomenon were studied. It was found that: (1) the activity of RNA polymerase I in the nuclei of livers from re-fed animals showed an enhancement of about 2-fold compared with the activity in normal and protein-depleted liver nuclei; (2) ribosome degradation, measured by the disappearance of radioactivity from ribosomal proteins previously labelled by the administration of NaH14CO3 to the mice, stopped during the first day after re-feeding.

Synthesis and conservation of ribosomal proteins during compensatory renal hypertrophy

The rate of synthesis of ribosomal proteins was investigated as an index of the rate of production of ribosomes in mouse kidney during the first few days after contralateral nephrectomy. Compensatory renal hypertrophy was not associated with a major increase in the synthetic rate of ribosomal proteins and rRNA. Instead, the ratio of the rate of ribosomal-protein synthesis to that of total protein synthesis remained nearly constant. The conformation of glutaraldehyde-fixed ribosomes and ribosomal subunits was unchanged. During the early stages of compensatory renal hypertrophy the accretion of rRNA is due largely to conservation of ribosomes that would otherwise have been degraded.

Presence of renotrophic factor in plasma of unilaterally nephrectomized rats

1. Renal cortical slices cut in two halves were incubated separately in culture medium. One half slice was used as control while the other half was treated experimentally. After incubation, their dry weights and/or their protein content were estimated. 2. Addition to half cortical slices of 30 micrograms mg-1 of freeze-dried plasma from rats killed 24 hr after unilateral nephrectomy resulted in an increase of dry weight or protein content of the order of some 10% after 4-8 hr incubation. 3. The effect of freeze-dried plasma from rats killed 24 hr after unilateral nephrectomy was specific to the renal cortex. When added to half slices from either the renal medulla or the liver there were no changes in their dry weight. 4. Addition of 30 micrograms mg-1 of freeze-dried plasma from rats killed 24 hr after bilateral nephrectomy had no significant effect on the dry weight of half cortical slices incubated for various periods of time, from 4 to 48 hr. 5. The renotrophic activity of plasma from unilaterally nephrectomized rats, killed 24 hr after the operation, appears to be metabolized or destroyed by incubation with cortical slices in 4 hr. 6. Freeze-dried plasma from normal unilaterally nephrectomized rats produced an increase dry weight when incubated for 4 hr with half cortical slices from early (3 days) hypophysectomized rats. When incubated with half cortical slices from late (23 days) hypophysectomized rats, the increase in dry weight was about 2 times as great as that observed with cortical slices from normal animals. 7. The possible reason for the production of renotrophic activity in plasma of unilaterally nephrectomized rats, and for its absence in plasma of anephric animals, is discussed.

The measurement of colonic mucosal-submucosal blood flow in man

1. A method is described for the measurement of colonic mucosal-submucosal blood flow in man, by studying surgically created colostomies. 2. A local radioisotopic clearance technique utilizing a stable preparation of [125I]4-iodoantipyrine is employed. The indicator is injected directly into the colostomy under study and its gamma emission is recorded by a scintillation detector. 3. A radioautographic study was carried out at laparotomy in humans to facilitate the interpretation of the recorded washout curves. This demonstrated that the tracer was cleared from both the mucosa and submucosa throughout the period of study. 4. Mucosal-submucosal blood flow was calculated according to Kety (1949) from the monoexponential clearance curves obtained, and amounted to 31.7 +/- 11 ml./min. 100 g (S.D. of an observation, n = 30). 5. The results from two consecutive measurements in seventeen patients showed that the mean change between first and second readings was not significant (t test). In addition the between-patient variation (12.2) was significantly greater than the within-patient variation (2.6) for consecutive recordings (F test; P less than 0.01). 6. The within-patient between-days variation (12.9; n = 10) was found to be similar to the between-patient variation. 7. It is concluded that the technique permits measurement of local colonic blood flow in man and by consecutive measurements, it may be used to evaluate local changes in blood flow following reflex or pharmacological stimulation.

Incorporation of exogenous precursors into uridine nucleotides and ribonucleic acid. Nucleotide compartmentation in the renal cortex in vivo

The possibility of compartmentation of UTP in vivo was investigated in the renal cortex of unanaesthetized rats. In addition, liver and spleen were studied in order to compare tissues with different utilization of precursors for pyrimidine nucleotide synthesis. After continuous 2h infusions of [(3)H]uridine or [(3)H]orotate, their incorporation into UTP, UDP-sugars and RNA was quantified. Rates of RNA synthesis were calculated by dividing the incorporation of precursor into RNA by the average specific radioactivity of the UTP pool. Although similar RNA-synthesis rates might have been expected with the two precursors, higher rates were found with uridine than with orotate. The relative incorporation into UDP-sugars of these precursors was also different. Similar results were obtained in the liver. In the spleen, equal amounts of both precursors were incorporated into UTP, but [(3)H]orotate incorporation did not lead to labelling of RNA. To evaluate the heterogeneity of cells with respect to the metabolism of pyrimidines, precursor incorporation was studied in isolated glomeruli and by radioautography. Incorporation into glomeruli was qualitatively similar to but quantitatively different from results in the renal cortex. Although there is obvious tissue heterogeneity, compartmentation of UTP pools is the most credible explanation for the results obtained with the renal cortex and liver. Consequently RNA and UDP-sugars may originate from two different UTP pools. Tissue heterogeneity is the likely explanation for the results obtained in the spleen. Studies of synthesis of pyrimidine and RNA, particularly in relation to growth and regeneration, must take into consideration the precursor used, the apparent existence of UTP compartmentation and the degree of cellular heterogeneity.

Onset of ribosome degradation during cessation of growth in BHK-21/C13 cells

When BHK-21/C13 cells growing exponentially in 10% serum are transferred to a medium containing only 0.25% serum, cell growth is decreased. After initial changes in RNA synthesis and degradation, protein content of the cultures reaches a plateau and eventually DNA synthesis is arrested. rRNA is relatively stable in exponentially growing cells. Immediately after 'step-down' rRNA degradation commences, but poly(A)-containing RNA does not appear to be degraded any faster than in control cells. Reutilization of RNA precursors has been independently measured and amounts to less than 1%/h for rRNA, insufficient to influence the conclusion that rRNA degradation begins almost immediately after 'step-down'. The degree of reutilization of uridine is much greater for poly(A)-containing RNA than for poly(A)-free RNA.

Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography

Isolation of newly synthesised RNA can be achieved by treatment of cells in culture with 6-thioguanosine or 4-thiouridine followed by separation of thiol-containing RNA by affinity chromatography on mercurated cellulose columns. After short periods of treatment with 6-thioguanosine the proportion of RNA retained on mercurated cellulose is the same for both poly(A)-containing and poly(A)-free RNA, indicating similar incorporation of the drug into mRNA and rRNA. However, after longer periods of exposure, the cytotoxic effect of 6-thioguanosine results in diminished incorporation of radioactive uridine into RNA and of radioactive leucine into protein; this suggests that synthesis of both RNA and protein are impaired. On the other hand, even after long exposure to high concentrations of 4-thiouridine, the syntheses of RNA and protein are not significantly affected. Proteins synthesised after treatment of cells with 6-thioguanosine are less stable than proteins synthesised after treatment of cells with 4-thiouridine.

Messenger RNA in compensatory renal hypertrophy

Experiments that deal with the stability of messenger RNA (mRNA) in normal mouse kidney, and, to some extent, the stability of mRNA during renal growth will be described. We have found a population of mRNA in the cytoplasm of mouse kidney that is short-lived. Such a class of rapidly metabolized mRNA could play an adaptive role at the translational or cytoplasmic level in determining gene expression and may be important during the early phases of compensatory hypertrophy.

Macromolecular metabolism in compensatory renal hypertrophy

1. The initial biochemical changes of compensatory hypertrophy occur well within 1 hour of unilateral nephrectomy and perhaps within the first few minutes.2. The initial increment in rRNA is from decreased metabolism rather than from increased synthesis.3. Changes in the processing of mRNA precursors are probably also important.4. Compensatory hypertrophy is regulated by a humoral stimulus or stimuli.5. The stimulus needs to be present virtually all of the time during the early phases of compensatory hypertrophy.6. The stimulus is related to loss of renal mass, not to loss of renal function.

Ribosomal proteins of mouse kidney: normal status and during compensatory renal hypertrophy

Ribosomes were isolated from normal and growing kidney and the protein complement was examined by a two-dimensional gel electrophoretic procedure. Proteins were resolved in the first dimension on the basis of charge and, in the second dimension, on the basis of molecular weight. 60S and 40S ribosomal subunits from normal kidney contained respectively 42 and 31 proteins. 80S ribosomes contained 23 proteins not found with either sub-unit. Nineteen of these proteins were removed from the ribosomes when isolated ribosomes were washed in a high salt buffer. Six proteins of the 80S ribosome corresponded to proteins associated with both sub-units. 80S ribosomal proteins were also studied during compensatory renal hypertrophy after 4-96 h of induced growth. The protein complement displayed by electrophoresis was identical to the pattern seen from normal renal cells.

Short-lived methylated messenger RNA in mouse kidney

In experiments originally designed to examine selective turnover of methylated "caps" in renal mRNA, we observed that [3H]methyl label decayed from mRNA containing poly(A) with a half-life of 1-2 hr. (Caps are blocked, methylated mRNA sequences of the general structure m7GpppNm p(1 or 2)Np.). To distinguish between metabolism of short-lived mRNA and discriminate turnover of "caps", we compared residual [3H]methyl label in 5' and 3'mRNA fragments prepared from mRNA isolated during the decay period. Hydrolysis of mRNA at 0 degrees with dilute KOH before oligo(dT)-cellulose selection produced 5' mRNA fragments enriched with an alkali-resistant oligonucleotide with a -5 charge; the 3' mRNA fraction was correspondingly reduced in oligonucleotide content. Since methyl label disappeared at the same rate from both fractions, we conclude that mouse kidney contains short-lived mRNA and that the "caps" of these labile mRNAs turn over with the rest of the mRNA molecule.

Accumulation and decay of messenger ribonucleic acid in mouse kidney

The stability of polyadenylated messenger ribonucleic acid(mRNA) from cytoplasmic structures sedimenting faster than 40S was analyzed in normal mouse kidney. Incorporation of radioactivity into poly(A)-containing and poly(A)-lacking cytoplasmic RNAs separated by oligo(dT)-cellulose chromatography was determined after sedimentation of RNA IN SODIUM DODECYL SULFATE CONTAINING SUCROSE DENSITY GRADIENTS. Radioactivity accumulated in poly(A)-containing RNA during the first 6 h and then decayed exponentially. Beginning 8-12h after administering label, two components were evident in the decay curve of poly(A)-containing RNA; the short-lived component (approximately 57% of newly synthesized molecules) had an apparent half-life of 6h, and the second class (approximately 43% of new mRNA) was more stable, decaying with a 24-h half-life. These studies provide the basis for examining the regulation of mRNA stability during compensatory renal hypertrophy.