Messenger ribonucleic acid metabolism in mammalian mitochondria: relationship between the decay of mitochondrial mRNA and their poly(A).

The mitochondrial poly(adenylic acid)-containing mRNAs in mouse ascites cells pulsed with radioactive precursors contain 35-55 nucleotide long poly(adenylic acid) sequences. These sequences are shortened with age in cells chased with cold medium. The possible relationship between the decay rates of mRNA and their poly(adenylic acid) sequences has been investigated by using mitochondrial RNA and protein synthesis inhibitors. The pattern of mRNA decay as determined by a new solid-phase-bound complementary DNA procedure indicates the presence of two classes of poly(adenylic acid) containing mRNA in mammalian mitochondria: one decaying with a t1/2 of 45 min and the other class with a t1/2 of 210 min. Inhibitors such as ethidium bromide and puromycin which accelerate the decay of mitochondrial mRNA also cause an enhanced decay of poly(adenylic acid) sequences. These results have been interpreted as evidence supporting the involvement of poly(adenylic acid) sequences in the mRNA stability.     

Post-fertilization polyadenylation during transcriptive and translational inhibition

Actinomycin D and ethidium bromide do not suppress the transition in the size distribution of poly (A)-containing RNA which normally occurs between fertilization of the sea urchin egg and the four-cell stage of development. In contrast, curtailment of post-fertilization protein synthesis by emetine alters this processive pattern of adenylation. Within the limits imposed by the $\text{in vivo}$ use of antimetabolites, these findings suggest that the observed cytoplasmic polyadenylation is subject to translational control.     

The synthesis of polyadenylic acid-containing ribonucleic acid by isolated mitochondria from Ehrlich ascites cells.

The synthesis of poly(A)-containing RNA by isolated mitochondria from Ehrlich ascites cells was studied. Isolated mitochondria incorporate [3H]AMP or [3H]UTP into an RNA species that adsorbs on oligo (dT)-cellulose columns or Millipore filters. Hydrolysis of the poly(A)-containing RNA with pancreatic and T1 ribonucleases released a poly(A) sequence that had an electrophoretic mobility slightly faster than 4SE. In comparison, ascites-cell cytosolic poly(A)-containing RNA had a poly(A) tail that had an electrophoretic mobility of about 7SE. Sensitivity of the incorporation of [3H]AMP into poly(A)-containing RNA to ethidium bromide and to atractyloside and lack of sensitivity to immobilized ribonuclease added to the mitochondria after incubation indicated that the site of incorporation was mitochondrial. The poly(A)-containing RNA sedimented with a peak of about 18S, with much material of higher s value. After denaturation at 70 degrees C for 5 min the poly(A)-containing RNA separated into two components of 12S and 16S on a 5-20% (w/v) sucrose density gradient at 4 degrees C, or at 4 degrees and 25 degrees C in the presence of formaldehyde. Poly(A)-containing RNA synthesized in the presence of ethidium bromide sedimented at 5-10S in a 15-33% (w/v) sucrose density gradient at 24 degrees C. The poly(A) tail of this RNA was smaller than that synthesized in the absence of ethidium bromide. The size of the poly(A)-containing RNA (approx. 1300 nucleotides) is about the length necessary for that of mRNA species for the products of mitochondrial protein synthesis observed by ourselves and others.     

Nuclease activity in preparations of creatine phosphokinase: effect on mRNA stability

Creatine phosphokinase is used to generate ATP with creatine phosphate for $\text{in vitro}$ protein synthesis. Some preparations of this enzyme contain nuclease activity, which can be demonstrated by a sensitive assay of the cleavage of poly(A)-containing RNA. These preparations of creatine phosphokinase support protein synthesis poorly in a cell-free system prepared from HeLa cells. Poly(A)-containing RNA is quite stable in this cell-free system when the phosphorylated sugar fructose 1,6-bisphosphate with no addition of enzyme is used to generate ATP.     

Peptidyl transferase substrate activity and inhibition of protein biosynthesis by a hydrophilic-aminoacyl analogue of puromycin.

A puromycin analogue possessing a hydrophilic amino acid, 3′-N-[S-(6-hydroxyhexyl)-$\text{L}$-cysteinyl]puromycin aminonucleoside, has been prepared and examined as a substrate for ribosomal peptidyl transferase. Kinetic studies indicate that this non-aromatic aminoacyl analogue is 95.6% as efficient as the parent antibiotic in the transpeptidation reaction. In addition, the analogue is an effective inhibitor of poly (U) and poly (U,C) directed protein synthesis in an $\text{Escherichia coli}$ cell free system.     

Primer directed poly(A) synthesis in rat liver mitochondria

Rat liver mitochondria contain an endogenous factor highly specific in stimulating the homologous poly(A) polymerase. By using an $\text{in vivo}$ labelling with [³²P] orthophosphate it is possible to prepare a labelled factor and to demonstrate that it is stably incorporated in an acid insoluble molecule. This suggests that the factor probably acts as a primer in the polymerization of ATP molecules, being involved in the recognition between the mitochondrial poly(A) polymerase and the homologous RNA molecules which have to be polyadenylated.     

The lognormal distribution fits the decay profile of eukaryotic mRNA.

A general program was written which simulates radioactive labeling of RNA $\text{in vivo}$. The program was used to determine the effect that different distributions of half-lives would have on the composite decay curve observed in a pulse-chase experiment. Four biologically relevant points emerge: 1) The published, experimentally determined composite decay curves for eukaryotic mRNA are not compatible with a normal, uniform, or exponential distribution of decay times. 2) The experimental curves are compatible with a lognormal distribution of decay times as well as the two-component discrete distribution previously hypothesized. 3) If the lognormal or some similar distribution were correct, about half the mRNA species would decay faster than what is presently called the “fast component of decay”. This point is crucial to any argument about the fraction of poly (A) or other nuclear sequence that is transported to the cytoplasm. 4) If a $\text{particular}$ mRNA species is found to decay at a constant rate for 3 half-lives, that is not only consistent with 1 half-life for all the mRNA, but also consistent with 20 different half-lives which are normally or uniformly distributed.In addition to the decay of mRNA, the lognormal distribution is also compatible with data on the decay of poly(A)-containing nuclear RNA and total cellular protein.     

Respiratory control and mitochondrial monovalent cation permeability of isolated liver cells

Uncoupling agent releases the respiratory control of rat hepatocytes to approximately the same degree as in isolated mitochondria indicating that mitochondria $\text{in situ}$ possess a low H⁺ conductance as $\text{in vitro}$. Mitochondria also have no detectable natural K⁺ conductance since the ionophore, valinomycin, is required for K⁺ ions to uncouple. Na⁺ but not K⁺ or choline inhibits the uncoupled respiration of liver cells. This is consistent with operation of neutral mitochondrial Na⁺ for H⁺ exchange $\text{in vivo}$. These results indicate a considerable similarity between certain functional and permeability properties of mitochondria $\text{in vitro}$ and $\text{in situ}$. These similarities form the basis for discussion of the role of mitochondrial ion transport in metabolic regulation.     

Protein synthesis in mitochondrial and microsomal fractions from rat brain and liver after acute or chronic ethanol administration

Incorporation of C¹⁴ Leucine was determined $\text{in vitro}$ or $\text{in vivo}$ in isolated mitochondria and microsomes of rat brain and liver after acute or chronic ethanol administration $\text{in vivo}$.The protein synthesis in mitochondrial and microsomal preparation was inhibited respectively by chloramphenicol and cycloeximide, specific inhibitors for the two systems tested. The experimental data demonstrate that the $\text{in vitro}$ protein synthesis in both systems, mitochondrial and microsomal, is strongly affected only after chronic treatment which produces significant activation at the mitochondrial and microsomal level in the liver and an inhibition on the same systems of the brain.The data for $\text{in vivo}$ protein synthesis instead show strong inhibition after acute administration, except for brain mitochondria, which are practically unaffected, while after chronic treatment no significant alterations are observed.     

RNA synthesis in Escherichia coli during K + -depletion

During K⁺ depletion of a mutant of $\text{Escherichia}$$\text{coli}$ which cannot concentrate this cation, protein synthesis is inhibited but RNA formation continues. The RNA produced during K⁺ depletion was analyzed by gel electrophoresis. It was found that 4S, 5S and 23S RNA were synthesized by K⁺-depleted cells whether uninfected or infected with phage T4. In addition, an RNA species moving close to 16S (presumably 17S) and material of about 6–10S were made during K⁺ depletion. These species of RNA were not evident in growing cells. Methylation of RNA is severely inhibited during K⁺ depletion.     

Functional efficiency of mitochondrial membrane of rats with hepatic chronic iron overload

The effect of $\text{in}\text{vivo}$ hepatic iron overload, induced by two different amounts of iron, on the energy-transducing efficiency of the mitochondrial membrane has been examined. It has been found that when the epatic iron concentration is up to a threshold value mitochondria present an anomalous membrane potential. Addition of oligomycin fully restitutes it. A low content of intramitochondrial K⁺ is connected with this pathological condition. A relative lack of antioxidant capability is parallely exhibited by these mitochondria. A possible involvement of lipid peroxidation process $\text{in}\text{vivo}$ in causing the membrane potential drop and the net efflux of intramitochondrial K⁺ is suggested.     

Biochemical studies of mammalian oogenesis: synthesis and stability of various classes of RNA during growth of the mouse oocyte in vitro

The synthesis of various classes of RNA in mouse oocytes at different stages of growth has been examined after incubating follicles in medium containing radiolabeled uridine. After fractionation on poly(U)-Sepharose of radiolabeled oocyte RNA, of which about 83% is associated with the nucleus after a 5-hr labeling period, revealed that about 40–50% of the radiolabeled RNA behaved as poly(A)-containing RNA. This value remained fairly constant during the period of oocyte growth in which oocyte diameter increased from about 35 to about 55 μm. After a 5-hr labeling, the percentage of radiolabeled poly(A)-containing RNA in either the fully grown dictyate oocyte, metaphase II oocyte, or one-cell embryo was about 20%. After a 5-hr labeling, agarose gel electrophoretic analysis of the radiolabeled species of oocyte RNA obtained after fractionation on poly(U)-Sepharose revealed the presence of a putative ribosomal RNA precursor, ribosomal (28 and 18 S) RNA, transfer plus 5 S RNA and heterodisperse poly(A)-containing RNA. A significant fraction of the radiolabeled RNA species was quite large (>40 S). The ratios of the relative proportions of the radiolabeled ribosomal RNAs and transfer plus 5 S RNA remained essentially constant during oocyte growth. The stability of various classes of RNA was examined by incubating follicles with radiolabeled uridine, washing the follicles free of radioactivity and culturing the follicles under conditions which support oocyte growth in vitro (Eppig, 1977). Under these conditions, total oocyte radiolabeled RNA was quite stable as determined by retention of acid-insoluble radioactive material ($\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 28}\text{days}$). However, under conditions in which oocytes are viable but do not grow, the half-life of total RNA was about 4.5 days. Poly(A)-containing RNA was also very stable; after 8 days in culture, about 50% of the radiolabeled poly(A)-containing RNA present after 5 hr of labeling was still present. Agarose gel electrophoretic analysis of radiolabeled RNA in oocytes after 4 days of culture and after fractionation on poly(U)-Sepharose revealed the presence of ribosomal (28 and 18 S) RNA, transfer plus 5 S RNA, and heterodisperse poly(A)-containing RNA. At this time, these RNAs are located in the oocyte cytoplasm. In addition, the molecular weight distribution of poly(A)-containing RNA was significantly lower than that after 5 hr of labeling. The ratios of the relative proportions of radiolabeled ribosomal RNAs and transfer plus 5 S RNA were quite similar to those after 5 hr of labeling.     

The synthesis of proteolipid protein by isolated rat liver mitochondria

About 15% of the total (³H)leucine incorporated into protein by isolated rat liver mitochondria $\text{in}\text{vitro}$ could be extracted by chloroform:methanol. This incorporation was inhibited by chloramphenicol and carbomycin, both specific inhibitors of mitochondrial protein synthesis. SDS-gel electrophoresis of the mitochondrial membrane revealed 6–7 labeled bands. Label in the proteolipid fraction was present mainly in a band of 40,000 molecular weight. Several labeled bands observed in gels of the mitochondrial membrane were not removed or changed by extraction with chloroform:methanol suggesting that some, but not all, of the proteins synthesized by rat liver mitochondria are proteolipids.     

Unmasking the mitochondrial K/H exchanger: swelling-induced K+-loss.

Matrix swelling induces a rapid, transient, energy-independent potassium efflux in rat liver mitochondria. Swelling-induced K⁺-loss is electroneutral; therefore it does not reflect electrophoretic diffusion secondary to increased membrane permeability. Matrix swelling unmasks an endogenous $\text{K}\text{H}$ transport mechanism in the mitochondrial membrane, providing a valuable experimental approach to the study of K⁺ transport in mitochondria.     

A template independent, rifampicin sensitive poly (A).poly (U) synthesizing activity present in Bacillus subtilis.

A template independent poly (A)·poly (U) synthesizing activity has been isolated from $\text{Bacillus subtilis}$. This activity is eluted from a DNA-cellulose column along with DNA-dependent RNA polymerase. The column fractions which exhibit this activity contain RNA polymerase holoenzyme plus a polypeptide which is slightly larger than sigma factor; pure RNA polymerase holoenzyme did not synthesize poly (A)·poly (U). The activity was dependent on the presence of ATP, UTP, and Mn⁺⁺ (Mg⁺⁺ could not substitute), and was inhibited by rifampicin, streptolydigin, and Cibacron Blue. The incorporation of nucleotides was not linear with time, but appeared after a lag period. The results suggest that a modified form of DNA-dependent RNA polymerase analogous to $\text{Escherichia coli}$ holoenzyme II is catalyzing the synthesis of poly (A)·poly (U).     

Expression and subcellular distribution of mouse cytochrome P1-450 mRNA as determined by molecular hybridization with cloned P1-450 DNA

Cytochrome P₁-450 (P₁-450) is defined as that cytochrome most closely associated with 3-methylcholanthrene (MC)-induced aryl hydrocarbon hydroxylase (AHH) activity. Recently a cloned DNA sequence (clone 46) was shown to represent a portion of the P₁-450 structural gene [Negishi $\text{et}\text{al.}\text{,}\text{Proc. Nat. Acad. Sci. U.S.A.}\text{78}$: 800–804 (1981)]. Poly(A⁺)-enriched RNA was isolated from total liver homogenate, membrane-bound polysomes and from free polysomes at various times after MC treatment of $\text{Ah}$-responsive $\text{C57BL}\text{6N}$ (B6) and $\text{Ah}$-nonresponsive $\text{DBA}\text{2N}$ (D2) inbred mice. The poly(A⁺)-enriched RNA was separated by methylmercury-agarose gel electrophoresis and hybridized to nick-translated [³²P]DNA from clone 46. By means of this RNA-DNA hybridization, only 6% of total polysomal P₁-450 mRNA exists in free polysomes after 24 h of MC treatment. The data indicate that the endoplasmic reticulum is the principal site of synthesis for this integral microsomal protein.Studies of induction kinetics following MC treatment provided the evidence of the rapid increase of total liver and membrane bound P₁-450 mRNA preceding the synthesis of apo-P₁-450 and the increase of AHH activity.     

Synthesis of diphtheria toxin in E. coli cell-free lysate

An $\text{E. coli}$ cell-free lysate was used to translate $\text{C. diphtheriae}$ RNA from nontoxinogenic C₇(?), C₇ infected with β tox⁺ corynebacteriophage, and $\text{C. diphtheriae}$ strain PW8. De novo synthesis of toxin was detected by immune precipitation with antitoxin, ADP-ribosylation of mammalian elongation factor 2 and rabbit skin test. The results indicated that toxin is produced in the $\text{E. coli}$ protein synthesizing system primed with RNA from cells infected with tox⁺ bacteriophage and is absent in systems primed with RNA from C₇(?) cells.     

RNA polymerase activity in double-stranded ribonucleic acid virus particles from Aspergillus foetidus.

RNA polymerase activities have been detected in purified particles of $\text{Aspergillus foetidus}$ viruses S and F. Incorporation of [³H]-UTP into acid insoluble RNA was dependent on ATP, GTP, CTP and magnesium ions. No pretreatment of the particles was required and the rate of reaction was proportional to the amount of virus added. In the conditions used RNA synthesis by $\text{A. foetidus}$ virus S was complete in 4 h. The reaction could be stimulated by Triton X-100, but was unaffected by heat shock, dithiothreitol, potassium chloride or ammonium chloride; it was inhibited by ethidium bromide but not by actinomycin D. The major reaction product was single-stranded RNA, as indicated by its sensitivity to degradation by ribonuclease A. This is the first report of synthesis of single-stranded RNA by a double-stranded RNA mycovirus.