Cloned complementary deoxyribonucleic acid probes for untranslated messenger ribonucleic acid components of mouse sarcoma ascites cells

Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR

In transfection experiments with mammalian cells aiming to overexpress a specific protein, it is often necessary to correctly quantify the level of the recombinant and the corresponding endogenous mRNA. In our case, mouse calvarial osteoblasts were transfected with a vector containing the complete Pex11β cDNA (plasmid DNA). The Pex11β mRNA level, as calculated using the RT-qPCR product, was unrealistically higher (>1000-fold) in transfected compared to non-transfected cells, and we assumed that there were large amounts of contaminating plasmid DNA in the RNA sample. Thus, we searched for a simple way to distinguish between plasmid-derived mRNA, endogenous genome-derived mRNA and plasmid DNA, with minimal changes to standard RT-PCR techniques. We succeeded by performing a plasmid mRNA-specific reverse transcription, and the plasmid cDNA was additionally tagged with a nonsense tail. A subsequent standard qPCR was conducted using appropriate PCR primers annealing to the plasmid cDNA and to the nonsense tail. Using this method, we were able to determine the specific amount of mRNA derived from the transfected plasmid DNA in comparison to the endogenous genome-derived mRNA, and thus the transfection and transcription efficiency.

Molecular cloning and expression characterization of translationally controlled tumor protein in silkworm pupae

A Bombyx mori (B. mori) cDNA was isolated from silkworm pupae cDNA library encoding a homologue of translationally controlled tumor protein (BmTCTPk). BmTCTPk was expressed in E. coli; SDS-PAGE and Western blot showed the molecular weight of recombinant and native BmTCTPk is approximately 28 and 25 kDa, respectively; they are larger than the theoretical molecular weight. Immunohistochemical studies showed that BmTCTPk is uniformly distributed throughout the cytoplasm of BmN cells. In silkworm pupae, BmTCTPk is expressed in the midgut wall, the midgut cavity, and some fat body tissues lying between the midgut wall and body wall. Western blot and ELISAs performed on total protein extracts isolated from silkworm pupae at different development stages showed that, although BmTCTPk is expressed during all pupae stages, its expression level increases dramatically during late pupae stages, suggesting that BmTCTPk may play an important role during the developmental transition from pupa to imago.

Translational control of specific genes during differentiation of HL-60 cells

Eukaryotic gene expression can be regulated through selective translation of specific mRNA species. Nevertheless, the limited number of known examples hampers the identification of common mechanisms that regulate translation of specific groups of genes in mammalian cells. We developed a method to identify translationally regulated genes. This method was used to examine the regulation of protein synthesis in HL-60 cells undergoing monocytic differentiation. A partial screening of cellular mRNAs identified five mRNAs whose translation was specifically inhibited and five others that were activated as was indicated by their mobilization onto polysomes. The specifically inhibited mRNAs encoded ribosomal proteins, identified as members of the 5'-terminal oligopyrimidine tract mRNA family. Most of the activated transcripts represented uncharacterized genes. The most actively mobilized transcript (termed TA-40) was an untranslated 1.3-kilobase polyadenylated RNA with unusual structural features, including two Alu-like elements. Following differentiation, a significant change in the cytoplasmic distribution of Alu-containing mRNAs was observed, namely, the enhancement of Alu-containing mRNAs in the polysomes. Our findings support the notion that protein synthesis is regulated during differentiation of HL-60 cells by both global and gene-specific mechanisms and that Alu-like sequences within cytoplasmic mRNAs are involved in such specific regulation.

Biogenesis and cell cycle relationship of poly(A)- actin mRNA in mouse ascites cells

A variety of rapidly growing mammalian cells contain a substantial portion of their actin mRNA in a poly(A)- form. We have used DNA-driven hybridization of a cloned actin cDNA-containing plasmid with pulse-labeled RNA from mouse S-180 ascites cells to examine newly synthesized actin mRNA. Our results indicate that the same proportion of newly synthesized and steady-state actin mRNA (approx. 40%) exists in a poly(A)- deficient form. This suggests that the poly(A)- form arises by some process other than slow cytoplasmic de-adenylation of a poly(A)+ precursor. We have also examined cell cycle-enriched populations of S-180 ascites cells for the presence of poly(A)- actin mRNA. Results from these experiments indicate that cells in G1 phase of the cell cycle contain predominantly poly(A)+ actin mRNA, while the poly(A)- form is restricted to late-S and post-S phase cells.

Level of translatable messenger RNA coding for argininosuccinate synthetase in the liver of the patients with quantitative-type citrullinemia

The translation activity of mRNA coding for argininosuccinate synthetase in total RNA extracted from the liver of three patients with quantitative-type citrullinemia was determined using a cell-free translation system. In two patients, the hepatic content of the enzyme was about 20% of the control value, whereas translatable mRNA level for the enzyme was similar to or slightly lower than those of control livers. In the third patient, the enzyme content was about 50% of the control value, and mRNA activity for the enzyme was low normal. These results indicate that at least in the first two patients, the decrease in the enzyme protein is due either to increased degradation of the enzyme or to decreased translation in the patient's liver.

Regulation of messenger RNA stability in mouse erythroleukemia cells

The decay rates of several messenger RNA species were determined in mouse erythroleukemia cells. The t1/2 values for the actin and tubulin mRNAs were 16 to 26 hours and about seven hours, respectively. The globin mRNA, and two mRNA species subject to translation repression, the P40 and P21 mRNAs, were about as stable as the ribosomal RNA. A stable tubulin mRNA component also appeared to be present in the cells. Exposure of the cells to dimethylsulfoxide for 48 hours led to considerable increases in the rates of decay of all but the globin mRNA. The induction of erythroid differentiation caused by the drug appears to lead to activation of a mRNA-degradation process that affects individual species to different degrees. The newly synthesized actin and tubulin mRNAs lost their poly(A) rather rapidly. This was accompanied by accumulation of poly(A)-deficient mRNA chains, particularly in the case of actin mRNA. The steady-state distribution of mRNA components, determined by Northern blot analysis, also showed that the actin mRNA and one tubulin mRNA species have a high proportion of poly(A)-deficient molecules. The globin, P40 and P21 mRNAs showed little tendency to lose their poly(A) sequence. The steady-state globin and P40 mRNAs also had a low proportion of chains depleted of poly(A). For all five species, the proportions of poly(A)-deficient chains in newly synthesized mRNA were about the same in uninduced and induced cells, in spite of the large decreases in mRNA stability in the induced cells. The lack of correlation between tendency to lose poly(A) and rate of mRNA decay, and the large accumulation of poly(A)-deficient molecules in the cases of the actin and tubulin mRNAs suggest that the stability of mRNA is not determined solely by the presence of poly(A) on the RNA chains. The behavior of the untranslated species in induced and uninduced cells also fails to support the notion of a relationship between translation and mRNA decay.

Configuration of beta-globin messenger RNA in rabbit reticulocytes. Identification of sites exposed to endogenous and exogenous nucleases

Masked and exposed sites in rabbit beta-globin messenger RNA were identified through S1 nuclease mapping of RNase T1 cleavage sites. Sites exposed to this enzyme were compared in deproteinized polysomal RNA and in mRNA in its native configuration in reticulocyte extracts. The analysis showed that most of the 3' non-coding region is well accessible to the enzyme, both in deproteinized RNA and in the cell extract. A possible protecting function for the poly(A) sequence is suggested by the fact that molecules with very short poly(A) segments were cleaved preferentially in this region. The G residues in the 5' non-coding region were inaccessible to RNase T1. A highly sensitive site adjacent to the initiation AUG codon was evident in the deproteinized RNA. This site was far less accessible to the enzyme in the mRNA associated with ribosomes in the cell extract. The first 150 nucleotides in the coding region showed very little susceptibility to digestion by the enzyme, in deproteinized RNA as well as in the cell extracts. Preparations of untreated mRNA showed the occurrence of truncated molecules, apparently generated by cleavage by endogenous nucleases. These cleavages were most prevalent in the two non-coding regions. They occurred at sites containing A-U sequences in the 3' non-coding region, and at sites with different sequences in the 5' non-coding region. Incubation of cell extracts at 37 degrees C did not cause any increase in these endogenous cleavages. It is suggested that they may have been generated in the intact cells, possibly as part of the mRNA degradation process in maturing reticulocytes.

Regulation of mRNA utilization in mouse erythroleukemia cells induced to differentiate by exposure to dimethyl sulfoxide

Mouse erythroleukemia cells contain several abundant mRNA species that occur to a considerable extent as untranslated molecules. For two of these species, which code for polypeptides P40 and P21, the proportion of molecules engaged in translation decreases rapidly after exposure of the cells to dimethyl sulfoxide. The extent of utilization of a third species, the P36 mRNA, is not altered. The rate of production of the P40 mRNA does not appear to be affected in the dimethyl sulfoxide-treated cells. The P21 mRNA appears to be produced in increasing amounts, leading to a large accumulation of untranslated molecules in the cytoplasm. The mRNA for actin remains nearly fully utilized during this process, but its intracellular concentration decreases, thus resulting in a reduction in the amounts present in polysomes. The results indicate that some mRNA species in mouse tumor cells are subject to a translational repression process that can serve to regulate selectively the extent of expression of the corresponding genes.

cDNA clones encoding cytoplasmic poly(A)+ RNAs which first appear at detectable levels in haploid phases of spermatogenesis in the mouse

We have isolated several cDNA clones encoding cytoplasmic poly(A)+ RNAs which are enriched in postmeiotic (haploid) spermatogenic cells in the mouse. Seventeen of 750 clones from a testis cDNA library hybridized more strongly to 32P-labeled cDNA copied from cytoplasmic poly(A) RNA of round spermatids than pachytene spermatocytes. Northern gel blots demonstrated that these 17 plasmids hybridized to RNA(s) approximately 0.5 kb (1 clone), 0.7 kb (13 clones), 0.8 kb (1 clone), and 0.9 kb (2 clones). Four plasmids hybridizing to RNAs 0.7 and 0.9 kb were further characterized by Northern blots. The levels of hybridization were about 10-fold greater with RNA from round spermatids, elongating spermatids and residual bodies than from pachytene spermatocytes from adult testis. These plasmids did not hybridize with cytoplasmic poly(A)+ RNA from sexually immature testis, adult liver, or brain, larger precursors in adult testis nuclear RNA, total RNA from cultured Sertoli cells, poly(A)- RNA from adult testis or the mouse mitochondrial genome. These results demonstrate that certain poly(A)+ RNAs are abundant in haploid cells but barely or not detectable in meiotic cells suggesting the accumulation of these RNAs in round spermatids requires transcription in haploid cells.

Regulation of mRNA utilization in mouse erythroleukemia cells induced to differentiate by exposure to dimethyl sulfoxide

Mouse erythroleukemia cells contain several abundant mRNA species that occur to a considerable extent as untranslated molecules. For two of these species, which code for polypeptides P40 and P21, the proportion of molecules engaged in translation decreases rapidly after exposure of the cells to dimethyl sulfoxide. The extent of utilization of a third species, the P36 mRNA, is not altered. The rate of production of the P40 mRNA does not appear to be affected in the dimethyl sulfoxide-treated cells. The P21 mRNA appears to be produced in increasing amounts, leading to a large accumulation of untranslated molecules in the cytoplasm. The mRNA for actin remains nearly fully utilized during this process, but its intracellular concentration decreases, thus resulting in a reduction in the amounts present in polysomes. The results indicate that some mRNA species in mouse tumor cells are subject to a translational repression process that can serve to regulate selectively the extent of expression of the corresponding genes.

Decrease in the levels of specific non-polysomal messenger ribonucleoproteins during the mouse sarcoma-180 ascites cell cycle

A few mRNAs in S-180 ascites cells are found as non-polysomal messenger ribonucleoprotein particles, whose translation is restricted both in vivo and in vitro. To determine if these mRNPs remain untranslated throughout the cell cycle we obtained S-180 ascites cells enriched in cell cycle stages by centrifugation through ficoll gradients. The "inactive" mRNA species were clearly present in the pre-polysomal fraction from S and pre-S phase cells, however they were not detected in the mRNP fraction from post S phase cells. Hybridization of a cloned cDNA probe for one of these species (P-40) to polysomal RNA from pre- or post-S phase cells demonstrated it was present in substantially higher concentrations in polysomes from post-S phase cells, consistent with its translation after S phase. We also observed that a poly (A)-minus form of the mRNA coding for actin was restricted to post S phase cells.

Messenger RNA species partially in a repressed state in mouse sarcoma ascites cells

Four major mRNA species of mouse sarcoma ascites cells, coding for polypeptides designated P65, P40, P36, and P21, occur predominantly as untranslated messenger ribonucleoprotein particles. Cloned cDNA probes were used to study their distribution in cytoplasmic extracts of these cells. A considerable portion of the mRNA molecules sedimented as small particles, whereas the rest was present in polyribosomes. In contrast, the actin mRNA was present almost exclusively in polyribosomes. Incubation of the ascites cells in culture medium, particularly after a starvation treatment, caused an enhancement in polypeptide chain initiation relative to elongation in these cells, as evidenced by a shift of ribosomes into the polyribosome fraction and by an increase in polyribosome size. Exposure of the cells to a low concentration of cycloheximide, an inhibitor of the elongation step, had a similar effect. The actin mRNA and the active P65, P40, P36, and P21 mRNA molecules were shifted to larger polyribosomes in the treated cells, but no shift of molecules from small particles to polyribosomes was observed. The incubation in culture also led to considerable increases in the proportion of P65 and P40 mRNA molecules in the untranslated state. The results indicate that the untranslated state cannot be attributed to poor initiation efficiency. It is suggested that a portion of the mRNA molecules is maintained in a repressed state and that mRNA repression may represent an important translation control process.