Differences in the level of plastid-specific tRNA's in chloroplasts and etioplasts of phaseolus vulgaris

Comparison of the chromatographic profiles of chloroplast and etioplast leucyl-tRNA's and valyl-tRNA's shows that the levels of plastid-specific tRNA species are relatively higher in the chloroplasts. This suggests that light can stimulate the synthesis of plastid-specific tRNA's in higher plants.     

Study of the maturation of 5 s RNA precursors in Escherichia coli

The existence of three precursors to 5 s RNA's (p5 s RNA's) has been confirmed. p5 s RNA's and mature 5 s RNA have different 5′-terminal sequences and produce the following 5′-terminal oligonucleotides: p5 s RNA-I:pAUUUG; p5 s RNA-II:pUUUG; p5 s RNA-III:pUUG; 5 s RNA:pUG. The results of experiments on pulse-labelled cells treated with actinomycin D, on chloramphenicol-inhibited cells, on various ribosome assembly-defective mutants and on the state of 5 s RNA in polysomes after a short labelling period, support the following conclusions. (1) p5 s RNA-I is the first identifiable precursor which appears during a pulse. (2) The amount of p5 s RNA-II, relative to those of the other p5 s RNA's, is very low at all times during pulse-chase experiments. On the contrary, it becomes significant during chloramphenicol inhibition and in one assembly-defective mutant under non-permissive conditions. (3) The maturation steps which lead to p5 s RNA-III and 5 s RNA normally occur after binding to 50 s subunit precursor particles and are, consequently, dependent upon protein synthesis. (4) The transition from p5 s RNA-III to 5 s RNA is a slow process, which is neither dependent upon nor required for the proper functioning of 50 s subunits in protein synthesis.     

Nonviral Interferon Inducers

Interferon production can be stimulated by a great variety of microbial and nonmicrobial agents other than viruses. The nonmicrobial inducers can be divided into polyanions, mitogens, and a miscellaneous category including the various endotoxins and antibiotics. The polyanions appear to require a stable, high molecular weight backbone and a high density of free anionic groups whether they are polynucleotides, plastics, or polysaccharides. Mitogen-induced interferon appears to be but one of a constellation of substances produced following lymphocyte transformation. The process of transformation can be stimulated either by specific immune recognition or non-specifically by phytohemagglutinin. Synthetic polynucleotide inducers are active; the thermostable, double-stranded RNA''s are much more active than the double-stranded DNA''s or 1-, 3-, or 4-stranded RNA''s. Some success has been obtained with potentiation of nucleotide inducers through the use of polycationic substances, complexing with a polysaccharide, concurrent administration of a metabolic antagonist, or substitution of phosphate by thiophosphate in the polynucleotide backbone. The stages in the interaction of interferon stimulating RNA and cells can be divided into three steps: first, binding to cell surface, next, a temperature dependent "recognition" step, and finally, degradation and utilization of monomers in cellular RNA synthesis; the critical recognition site has not yet been determined. The vast majority of cell-associated polynucleotide remains at the surface of the cell. Information from animal models resembling human diseases suggests that certain of these nucleotide inducers may have clinical usefulness in therapy or prophylaxis.     

Control of protein synthesis by a temperature-sensitive mutant of reovirus 3. I. Temperature-sensitive function of ts261-b mutant.

The ability of a temperature-sensitive (ts) mutant of reovirus, ts261-b, to synthesize virus-specific RNAs and proteins during infection at the nonpermissive temperature (37 degrees C) was investigated. The relative amounts of the mutant virus-specific single-stranded (ss) RNA''s and double-stranded (ds) RNA''s synthesized in cells at 37 degrees C were 20 to 25% as much as those synthesized in the wild-type virus-infected cells. The 10 segments of the mutant ds RNAs and the three size classes of the ss RNAs were synthesized in the usual proportions. The methylation of the mutant viral mRNA''s (ss RNAs) was not blocked at 37 degrees C in infected cells. A striking temperature-sensitive restricted function of the ts261-b mutant was expressed in the synthesis of the viral proteins. This study, which uses an in vitro protein-synthesizing system reconstituted with an endogenous polysomal fraction and a postribosomal supernatant from reovirus-infected cells, has demonstrated that the endogenous polysomes obtained from ts261-b mutant-infected cells at 37 degrees C are not active in the synthesis of the viral polypeptides of known molecular weights, and the amounts of the mutant viral polypeptides synthesized in vitro by these polysomes are 5 to 9% of those synthesized by the corresponding fraction from wild-type-infected cells. The impaired protein-synthesizing capacity of the mutant virus-specific polysomes can be restored during maintenance of the infected cells at 30 degrees C after shift-down from 37 degrees C. The in vitro synthesis of viral polypeptides of known size by the active endogenous polysomes derived from cells infected at the permissive temperature is accelerated by the addition of the postribosomal supernatant obtained from cells infected at the permissive temperature. The postribosomal supernatant from mutant-infected cells at 37 degrees C did not have a stimulatory effect, but rather, it inhibited in vitro viral protein synthesis.     

Differentiation of chick embryo cerebral hemispheres: a critical evaluation of a bulk preparation of neuroblasts and spongioblasts

Abstract— A critical evaluation of a previously described method of bulk preparation of neuroblasts and spongioblasts from chick embryo cerebral hemispheres furnished the following results.

• 1 A major loss of total RNA occurs during the preparation of the cell fractions.
• 2 The loss occurred mainly during the dissociation of the tissue and the following centrifugations.
• 3 The missing RNA's were found in the supernatants after cell centrifugation at low speed.
• 4 There was a selective loss of transfer RNA amounting to 70–80 per cent relative to ribosomal RNA.
• 5 The relative proportions of the 29, 18 and 5s ribosomal RNA's were constant, but there was a decrease in their proportion relative to heavy-molecular weight, rapidly-labelled nuclear RNA.
• 6 The ribosomal RNA's in the low-speed supernatant could be resedimented at 35,000 g whereas most transfer RNA could not.

The results are consistent with a loss of fragments of cytoplasm containing ribosomes and with additional extraction of transfer RNA during the preparation.     

Various molecular aspects of cytology and embryology

Our present knowledge of the cell structure, which is largely based on electron microscopy, is compared with what was known a few decades ago, when only light microscopy was available to the cytologist. The importance of cytochemical methods for the detection and localization of macromolecules (nucleic acids, proteins) is stressed. But it is pointed out that further analysis, with biochemical techniques, was required in order to understand the actual mechanisms of macromolecule synthesis in the cell (in particular, the relationships existing between nucleic acids and protein synthesis). The importance of genetical analysis in simple systems such as viruses and bacteria for the development of ‘molecular’ biology is then emphasized: in particular, the work of Avery identifying the ‘transforming principle’ with DNA, of Beadle leading to the ‘one gene, one enzyme’ theory, of the virologists who demonstrated that it is the nucleic acid component of viruses which carries the genetical information, have been of fundamental importance for the development of modern biology. No less important has been the work of the X-ray crystallographers (Crick and Watson, Perutz, Kendrew, etc.) who established the fine structure of nucleic acids and of proteins. A brief review and a schematic representation of present ideas regarding the control exerted by DNA on the synthesis of specific proteins are then given: the main characteristics of the different kinds of RNA's, their interactions for the formation of polysomes, the role of the latter in protein synthesis, the main principles of the genetic codes, are briefly summarized. But cells are, in many respects, more complicated than bacteria. The concepts of molecular biology cannot be applied to cell differentiation without a recognition of the greater complexity of animal and plant cells. They represent, however, a most useful and powerful guide for research in that area: for instance, many aspects of morphogenesis in the unicellular alga Acetabularia and in amphibian eggs can be explained on the assumption that messenger RNA's are produced by the nucleus and stored, in a stabilized form, in the cytoplasm during days or even weeks. This stability of messenger RNA's in eggs and algae is at variance with their short life in bacteria. The behaviour of non-nucleate fragments of Acetabularia is surprising in many respects: they are the site, not only of the synthesis of specific proteins, but even of RNA and DNA net synthesis. Such a synthesis of macromolecules, in the absence of the nucleus is probably linked to the presence of the chloroplasts in this alga: they contain DNA, can synthesize RNA and proteins, and can even increase in number in the absence of the nucleus. The presence of large amounts of DNA in the cytoplasm of many animal eggs raises a number of questions and might account for the extremely important role of the cytoplasm in the very early stages of embryonic development. It is concluded that none of the great problems of cell biology will be solved without the help of the techniques and the theoretical ideas which have been so fruitful for the simpler systems used by the molecular biologists.     

Denaturation of RNA with dimethyl sulfoxide

The denaturation of single-stranded and double-stranded RNA's in solutions with varying proportions of dimethyl sulfoxide has been followed by changes in absorbancy, optical rotation, and—with a double-stranded form of bacteriophage of MS2 RNA— infectivity for bacterial spheroplasts. By these criteria the RNA's studied, including the synthetic polynucleotide rG:rC, are completely denatured at room temperature in high concentrations of this solvent. In lower concentrations, the T_m of the RNA preparation is decreased only slightly as the dimethyl sulfoxide concentration is raised until a critical concentration is reached. The T_m falls sharply with small further increases in dimethyl sulfoxide concentration. Sedimentation studies can be conducted directly in these media. The determination of sedimentation velocity in 99% dimethyl sulfoxide containing 0.001M EDTA provides a reliable estimate of RNA molecular weights.     

The procollagen type III, alpha 1 (COL3A1) gene first intron expresses poly-A+ RNA corresponding to multiple ESTs and putative miRNAs

The mouse COL3A1 first intron is 9684 bp. RNA's of approximately 1.6 and 3.0 kb were detected by Northern hybridization analysis of poly‐A RNA from fetal mice and total RNA from suckling and adult mouse intestine using ³²P‐labeled, anti‐sense RNA synthesized from a mouse COL3A1 first intron, 5 prime region, 5.4 kb Xba I fragment (1655–7030 bp), recombinant plasmid (pPI5.4x). Expression of the 1.6 and 3.0 kb RNA's was significantly reduced in adult mouse intestine, indicating that these RNAs are developmentally regulated. “BLAST” analysis indicated that the mouse first intron 5 prime sequence has 94–100% identity to 13 mouse ESTs. These mouse first intron EST's lie within the 5.4 Xba I fragment of the mouse COL3A1 first intron. Two of the mouse first intron EST's have significant identity to known miRNA, mature sequences, mmu‐miR‐466f‐3P, mmu‐miR‐1187, and mmu‐miR‐574‐5P as well as others. Predicted targets for mmu‐miR‐466f‐3P include COL1A1, COL19A1, COL11A2, COL4A1, and COL4A5 indicating that COL3A1 intronic miRNAs may regulate the expression of other collagen genes in development. J. Cell. Biochem. 112: 541–547, 2011. © 2010 Wiley‐Liss, Inc.     

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

Background

A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy minimization with energy parameters based on the nearest-neighbor model and comparative analysis are the primary methods for predicting an RNA's secondary structure from its sequence. Version 3.1 of Mfold has been available since 1999. This version contains an expanded sequence dependence of energy parameters and the ability to incorporate coaxial stacking into free energy calculations. We test Mfold 3.1 by performing the largest and most phylogenetically diverse comparison of rRNA and tRNA structures predicted by comparative analysis and Mfold, and we use the results of our tests on 16S and 23S rRNA sequences to assess the improvement between Mfold 2.3 and Mfold 3.1.

Results

The average prediction accuracy for a 16S or 23S rRNA sequence with Mfold 3.1 is 41%, while the prediction accuracies for the majority of 16S and 23S rRNA structures tested are between 20% and 60%, with some having less than 20% prediction accuracy. The average prediction accuracy was 71% for 5S rRNA and 69% for tRNA. The majority of the 5S rRNA and tRNA sequences have prediction accuracies greater than 60%. The prediction accuracy of 16S rRNA base-pairs decreases exponentially as the number of nucleotides intervening between the 5' and 3' halves of the base-pair increases.

Conclusion

Our analysis indicates that the current set of nearest-neighbor energy parameters in conjunction with the Mfold folding algorithm are unable to consistently and reliably predict an RNA's correct secondary structure. For 16S or 23S rRNA structure prediction, Mfold 3.1 offers little improvement over Mfold 2.3. However, the nearest-neighbor energy parameters do work well for shorter RNA sequences such as tRNA or 5S rRNA, or for larger rRNAs when the contact distance between the base-pairs is less than 100 nucleotides.     

Regulation of ribonucleic acid synthesis in growing bacterial cells. II. Control over the composition of the newly made RNA

Studies have been made by base-ratio analysis and DNA-RNA hybridization of the pulse-labeled, nascent RNA in cells of Escherichia coli growing exponentially in minimal-glucose and Casamino acids-supplemented media, as well as during shift-ups or shift-downs between them. It is found that the cell varies the fraction of the newly made RNA given over to the synthesis of ribosomal and (presumably) transfer RNA under these different conditions. Furthermore, for cells in exponential growth or during shift-up, these values are in good agreement with the amount of “stable” RNA made as defined in the kinetic experiments in the accompanying paper. Thus under these conditions, there is no need to postulate the existence of a mechanism involving the rapid destruction of otherwise stable RNA's, a situation which may occur in shift-down or other growth conditions.     

Specificity of protein synthesis by bacterial ribosomes and initiation factors: Absence of change after phage T4 infection

Using several natural messenger RNA's—f2 RNA, Qβ RNA, T7 RNA, T4 early mRNA, T4 late mRNA and Escherichia coli RNA—ribosomes isolated from cells either 5 or 12 minutes after T4 infection direct synthesis of only 35 to 70% as much protein as do ribosomes from uninfected cells. However, with poly(U) or formaldehyde-treated f2 RNA message, both types of ribosomes work equally well. Experiments mixing salt-washed ribosomes and initiation factors from these cells show, in agreement with work of others, that the reduction with natural messages is due only to changes in the initiation factors.     

Raman spectral studies of nucleic acids. XI. Conformations of yeast tRNAPhe and E. coli ribosomal RNA in aqueous solution and in the solid state

Laser-excited Raman spectra of tRNA^Phe from yeast and of fractionated 16S and 23S rRNA from E. coli are reported for samples in aqueous solution and in the solid state. The Raman scattering spectrum of each RNA is not significantly altered by the change from an aqueous to a solid environment and displays the same characteristic frequencies and intensities associated with ordered polyribonucleotide structures. Unlike DNA, the backbone conformation of RNA thus appears to be largely insensitive to gross changes in the degree of hydration. Raman scattering from the phosphate group vibrations of aqueous tRNA_yeast^Phe is qualitatively and quantitatively the same as obtained from previously studied tRNA's and is indicative of a highly ordered conformational structure in which some 85% of the nucleotide residues are in ordered configurations. The major differences observed between spectra of tRNA and rRNA are attributed to differences in base composition of these RNA's.     

Antisense RNA regulation of the fatB iron transport protein gene in Vibrio anguillarum

We have recently identified an antisense RNA (RNAα) that regulates the expression of the fatA iron transport gene encoding the outer membrane receptor for the iron-anguibactin complex. In this work, we demonstrate that RNAα also inhibits the expression of fatB , which encodes a 35 kDa iron transport protein and has domains homologous to other periplasmic transport proteins. The expression of fatA and fatB is repressed under iron-rich conditions, in which RNAα is induced. RNAα is homologous to two-thirds of the coding region of fatB . By cloning RNAα coding sequences immediately downstream of a tet promoter, we were able to obtain constitutive expression of the antisense RNA. The cloned region contains approximately 83% of the 650 nucleotide RNAα and is complementary to only 51% of the fatB mRNA but is still capable of causing a repression of the expression of the fatB gene. Our results in this work demonstrate that RNAα probably affects the stability of the fatB -specific mRNA.     

Protein synthesis in transformed 3T3 cells permeabilized by exogenous ATP

Exogenous ATP has been shown to cause a rapid and reversible increase in permeability in transformed 3T3 cells (3T6 and SV3T3) but not in untransformed 3T3 cells. The cells remain viable, but lose intracellular acid-soluble pools. Treatment of transformed cells with ATP greatly reduces incorporation of ¹⁴C-leucine into protein, which is restored by the incubation of the cells with Dulbecco's modified Eagle's medium or by the external additions of certain ions and energy sources. tRNA is not required for the restoration of protein synthesis. In the permeabilized cells the energy for protein synthesis can be provided by glycolysis, oxidative phosphorylation, or direct addition of ATP. These studies demonstrate the usefulness of this method for studying the control of metabolism and macromolecular synthesis in monolayer cultures of transformed mammalian cells.     

Preparative Polyacrylamide-Agarose Gel Electrophoresis of Proteins and RNAS by the Use of New Device

Quantitatively reproducible results were obtained by using a new device for preparative gel electrophoresis combined with polyacrylamide-agarose composite gel. When an adequate gel-buffer system was selected according to the procedure described in this paper, proteins and RNA's were well separated and recovered. The new device for preparative gel electrophoresis and the method for preparation of polyacrylamide-agarose composite gel are presented together with the elution profiles of the recovered substances.