Specific dissociation of pea 25-S rRNA by hot-phenol treatment

A simple methodology for RNA isolation from bacteria by integration of formamide extraction and chitosan-modified silica purification

RNA isolation from bacteria is technically difficult due to the RNA characteristic of labile and vulnerable degradation. Many reagents were explored for cellular lysis and complete inhibition of RNase. However, the available methods for RNA isolation are either of low efficiency or time-consuming. Here, we developed a rapid and accessible protocol for RNA isolation that combined a simplified cell lysis and RNA release by formamide-based solution and RNA purification by chitosan-modified silica membrane for the first time. With this method, we obtained about ~ 28 μg of total RNA from 10⁸ Escherichia coli cells. The entire procedure can be done within 15 min without redundant pipetting steps. The purity of extracted RNA was comparable to that of commercial kits, but the cost was much lower. Furthermore, the yielded RNA was successfully used in downstream enzymatic reactions, such as reverse transcription and quantitative real-time PCR. This new method would be of benefit for an extensive range of gene expression analyses in bacterial organisms.

Size heterogeneity of ribosomal RNA in eukaryote evolution--1. rRNA molecular weights in species containing intact large ribosomal subunit RNA

1. The molecular weights of the two major rRNA species (L-rRNA, large ribosomal subunit RNA, and S-rRNA, small ribosomal subunit RNA) of a variety of deuterostomia, green plants and fungi have been investigated by gel electrophoresis in 99% formamide, pH 9; the overall pattern obtained under these conditions differs to some extent from that deduced by electrophoresis in neutral-salt solutions. 2. The molecular weights of the deuterostomian S-rRNA species have been conserved at a value of 0.65 X 10(6), whereas those of the L-rRNA have been kept at 1.40 X 10(6) in the lower species but have increased to 1.55 X 10(6) in birds and to 1.65 X 10(6) in mammals. 3. The molecular weights of the L-rRNA and S-rRNA components of the green plants (Dycotyledons, Monocotyledons and Gymnosperms) have been generally conserved at 1.30 X 10(6) and 0.65 X 10(6). 4. The molecular weight of the L-rRNA of the fungi has been conserved at 1.36-1.38 X 10(6), being 0.1 X 10(6) daltons heavier than that of the plants; the S-rRNA exhibits a limited degree of variability, ranging between 0.65 X 10(6) and 0.72 X 10(6).

Processing of the ribonucleic acid in the large ribosomal subunits of Urechis caupo

Ribosomal subunits were isolated from eggs or embryos of Urechis caupo, and the ribonucleic acid (RNA) was characterized by electrophoresis under denaturing conditions. The small ribosomal subunit contains a single 17S RNA sequence with a molecular weight of 6.20 X 10(5). The large ribosomal subunit contains four polynucleotide sequences. The 5S RNA has a molecular weight of 4.09 X 10(4). The 26S RNA complex isolated under nondenaturing conditions dissociates in the presence of formamide to yield a 5.8S RNA, molecular weight 5.46 X 10(4), and two approximately 17S and 17.5S RNA sequences with molecular weights of 6.04 X 10(5) and 6.61 X 10(5). The 17S and 17.5S RNAs of the large ribosomal subunits are formed in vivo from a 26S RNA precursor after assembly of the large ribosomal subunit. Large ribosomal subunits are transferred from the nucleus to the cytoplasm with the 26S RNA precursor intact. The hidden break to form the 17S and 17.5S RNAs is introduced in the cytoplasm. No intact 26S RNA could be detected in polysomes; this indicates that the conversion of the 26S RNA to the 17S and 17.5S RNAs may be required to produce large ribosomal subunits capable of participating in protein synthesis.

The ribosomes of Plasmodium berghei: isolation and ribosomal ribonucleic acid analysis

Ribosomes and high molecular weight ribosomal ribonucleic acid (rRNA) from the blood stages of Plasmodium berghei parasites were studied in preparations free from host ribosome contamination. Purified malarial ribosomes were isolated in high yield from a population of ultrastructurally intact, viable parasites by hypertonic lysis with Triton X-100 and differential centrifugation. These ribosomes were shown to be derived from active polysomes and could be dissociated into subunits by puromycin-0.5 M KCl treatment. Malarial rRNA extracted from purified 40S and 60S ribosomal subunits was characterized by electrophoretic, sedimentation and base ratio analyses. Like certain other protozoa, the P. berghei 40S ribosomal subunit possessed an exceptionally large RNA species (mol. wt 0.9 X 10(6), while RNA isolated from the parasite's 60S subunit (mol. wt 1.5 X 10(6)) was specifically 'nicked' to produce one large component (mol.wt 1.2 X 10(6)) and one small component (mol.wt 0.3 X 10(6)) in equimolar quantities. These rRNA's migrate identically on polyacrylamide gels after heating to 63 degrees C for 5 min or under denaturing conditions in the presence of formamide, indicating an absence of aggregation and non-specific degradation of the rRNA species. Base composition studies showed P. berghei rRNA to be low in guanosine and cytosine content, as is the case for protozoa generally.

Evolution of ribosomal RNA

1. The G + C content of ribosomal RNA of animals seems correlated with the length of periods required for maturation of those organisms. 2. In Protostomes of the animal kingdom, the size of the 28S rRNA molecule does not seem to correlate with the evolutionary stage of the organism. 3. Aphids and water-fleas as well as some protozoa have the 18S rRNA with mol. wt of 0.9 x 10(6) against an overwhelming pressure of evolution to conserve the rRNA molecule of 0.7 x 10(6) daltons. 4. All the Deuterostomes examined were distinguished from Protostomes by having the 28S rRNA's void of the hidden break at the central point. 5. Aphids and nematodes are exceptional Protostomes in that they have the 28S rRNA's without the hidden break. This was discussed in the light of the evolutionary stage of these organisms. 6. Molecular properties of chloroplast rRNA seem to evidence for endosymbiotic origin of this organelle. Mitochondrial rRNA differs considerably from prokaryotic rRNA with respect to molecular size and base composition.

Structure and biosynthesis of the ribosomal ribonucleic acids from the oncogenic bacterium Agrobacterium tumefaciens

The rRNA of the oncogenic bacterium Agrobacterium tumefaciens was extracted by several methods and analysed by polyacrylamide-gel electrophoresis. The large rRNA of this bacterium is degraded in vivo during the maturation of the ribosome. The influence of Mg2+ and denaturation on degradation of 23S RNA was studied. In pulse and chase experiments, we identified two precursors of the rRNA with mol.wts. of 1.04 x 10(6) and 0.70 x 10(6). From studies of the structure of the large rRNA, we propose that it could have arisen from a gene duplication. This structure is discussed in relation to a recent hypothesis involving such gene duplication as a means of origin of 23S rRNA.

Postmaturational cleavage of 23s ribosomal ribonucleic acid and its metabolic control in the blue-green alga Anacystis nidulans

Data are presented consistent with the notion that the 23s ribosomal ribonucleic acid (rRNA) of Anacystis nidulans undergoes specific endonucleolytic cleavage in vivo, to produce two fragments with molecular weights of 0.88 x 10(6) and 0.17 x 10(6) daltons. Cleavage occurred at random after 23s rRNA formation and was stimulated by light in this organism, an obligately photoautotrophic unicellular blue-green alga. The half-life of intact 23s rRNA was about 5 h in illuminated cultures and 10 h in unilluminated cultures. 3-(p-Chlorophenyl)-1, 1-dimethylurea, an inhibitor of photosystem II, retarded 23s rRNA cleavage in the light. The results are discussed in the context of recent reports of rRNA instability in a variety of eukaryotic and prokaryotic organisms.