Formation of all stable RNA species in Escherichia coli by posttranscriptional modification

Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders

Most of the sequences in the human genome do not code for proteins but generate thousands of non-coding RNAs (ncRNAs) with regulatory functions. High-throughput sequencing technologies and bioinformatic tools significantly expanded our knowledge about ncRNAs, highlighting their key role in gene regulatory networks, through their capacity to interact with coding and non-coding RNAs, DNAs and proteins. NcRNAs comprise diverse RNA species, including amongst others PIWI-interacting RNAs (piRNAs), involved in transposon silencing, and small nucleolar RNAs (snoRNAs), which participate in the modification of other RNAs such as ribosomal RNAs and transfer RNAs. Recently, a novel class of small ncRNAs generated from the cleavage of tRNAs or pre-tRNAs, called tRNA-derived small RNAs (tRFs) has been identified. tRFs have been suggested to regulate protein translation, RNA silencing and cell survival. While for other ncRNAs an implication in several pathologies is now well established, the potential involvement of piRNAs, snoRNAs and tRFs in human diseases, including diabetes, is only beginning to emerge. In this review, we summarize fundamental aspects of piRNAs, snoRNAs and tRFs biology. We discuss their biogenesis while emphasizing on novel sequencing technologies that allow ncRNA discovery and annotation. Moreover, we give an overview of genomic approaches to decrypt their mechanisms of action and to study their functional relevance. The review will provide a comprehensive landscape of the regulatory roles of these three types of ncRNAs in metabolic disorders by reporting their differential expression in endocrine pancreatic tissue as well as their contribution to diabetes incidence and diabetes-underlying conditions such as inflammation. Based on these discoveries we discuss the potential use of piRNAs, snoRNAs and tRFs as promising therapeutic targets in metabolic disorders.

Transfer RNA and human disease

Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA) genes are “hotspots” for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase), mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers), and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing). Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.

Total aminoacyl-transfer RNA pool is greater in liver than muscle in rabbits

Transfer RNA (tRNA)-charged amino acids are direct precursors of protein synthesis. Therefore, the amount and profile of amino acids in the aminoacyl-tRNA pool may be closely related to the rate of protein synthesis in the tissue. This study was designed to compare the aminoacyl-tRNA pools in liver and muscle, 2 distinct tissues with different rates of protein synthesis. Liver and muscle samples were taken from 6 rabbits and aminoacyl-tRNA was isolated with sequential acid-phenol:chloroform extraction, followed by total RNA and tRNA purification. Amino acids in the aminoacyl-tRNA pool were measured by HPLC after deacylation. Liver contained 3.4 times more tRNA than muscle (585 +/- 120 vs. 132 +/- 11 microg of tRNA/g of tissue; P < 0.001). Overall tRNA charging was also greater in liver (14.22 +/- 4.42 nmol of amino acids/mg of tRNA) than in muscle (7.00 +/- 1.76 nmol of amino acids/mg of tRNA) (P < 0.05). The greater availability and charging efficiency of tRNA in liver as compared with muscle may influence the extent to which amino acid precursor availability regulates protein synthesis in these 2 tissues.

Protein component of Bacillus subtilis RNase P specifically enhances the affinity for precursor-tRNAAsp

Ribonuclease P (RNase P) is an endonuclease that cleaves precursor tRNA to form the 5'-end of mature tRNA and is composed of a catalytic RNA subunit and a small protein subunit. The function of the protein component of Bacillus subtilis RNase P in catalysis of B. subtilis precursor tRNAAsp cleavage has been elucidated using steady-state kinetics, transient kinetics, and ligand affinity measurements to compare the functional properties of RNase P holoenzyme to RNase P RNA in 10 mM MgCl2, 100 mM NH4Cl. The protein component modestly affects several steps including </=10-fold increases in the rate constant for tRNA dissociation, the affinity of tRNA, and the rate constant for phosphodiester bond cleavage. However, the protein principally affects substrate binding, increasing the affinity of RNase P for pre-tRNAAsp by a factor of 10(4) as determined from both the ratio of the pre-tRNAAsp dissociation and association rate constants measured in 10 mM MgCl2 and a binding isotherm measured in 10 mM CaCl2 using gel filtration to separate enzyme-bound and free pre-tRNAAsp. Therefore, the main role of the protein component in RNase P is to facilitate recognition of pre-tRNA by enhancing the interaction between the enzyme and the 5'-precursor segment of the substrate, rather than stabilizing the tertiary structure of the folded RNA as has been observed for protein-facilitated group I intron self-splicing. Furthermore, the protein component maximizes the efficiency of RNase P under physiological conditions and minimizes product inhibition.

Processing of procaryotic ribonucleic acid

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Transfer ribonucleic acid synthesis during sporulation and spore outgrowth in Bacillus subtilis studied by two-dimensional polyacrylamide gel electrophoresis

The synthesis of transfer ribonucleic acid (tRNA) was examined during spore formation and spore outgrowth in Bacillus subtilis by two-dimensional polyacrylamide gel electrophoresis of in vivo 32P-labeled RNA. The two-dimensional gel system separated the B. subtilis tRNA's into 32 well-resolved spots, with the relative abundances ranging from 0.9 to 17% of the total. There were several spots (five to six) resolved which were not quantitated due to their low abundance. All of the tRNA species resolved by this gel system were synthesized at every stage examined, including vegetative growth, different stages of sporulation, and different stages of outgrowth. Quantitation of the separated tRNA's showed that in general the tRNA species were present in approximately the same relative abundances at the different developmental periods. tRNA turnover and compartmentation occurring during sporulation were examined by labeling during vegetative growth followed by the addition of excess phosphate to block further 32P incorporation. The two-dimensional gels of these samples showed the same tRNA's seen during vegetative growth, and they were in approximately the same relative abundances, indicating minimal differences in the rates of turnover of individual tRNA's. Vegetatively labeled samples, chased with excess phosphate into mature spores, also showed all of the tRNA species seen during vegetative growth, but an additional five to six minor spots were also observed. These are hypothesized to arise from the loss of 3'-terminal residues from preexisting tRNA's.

Synthesis of transfer RNA during the synchronous nuclear division cycle in Physarum polycephalum

1. The synthesis of tRNA during the synchronous nuclear division cycle in plasmodia of Physarum polycephalum has been investigated using an isotope dilution procedure and compared to the pattern of synthesis of rRNA. 2. The synthesis of both tRNA stops during mitosis. As the genes for the two types of RNA are not linked, this finding suggests that cessation of synthesis during nuclear division is a common characteristic of all types of transcription, supporting earlier work using pulse labelling and autoradiography to investigate the same problem.

Ribosomal protein-nucleic acid interactions. I. Isolation of a polypeptide fragment from 30S protein S8 which binds to 16S rRNA

Within the bacterial ribosome a large number of specific protein and rRNA interactions appear to be required for assembly of the particle and its subsequent function in protein synthesis. In this communication it is shown that it is possible to isolate cyanogen bromide digestion products from ribosomal 30S protein S8 which will interact stoichiometrically with 16S rRNA. In addition to this a small binding polypeptide was generated from S8-16S rRNA complexes which were treated with proteinase K. The digestion of the complex yields a "protected" fragment of protein S8 which binds to 16S-rRNA. The isolated fragment will reassociate with 16S rRNA. It is not displaced by other 30S ribosomal proteins and blocks the binding of intact S8 to 16S rRNA. The size the possible structure of the S8 protein binding site are discussed and compared with the binding of cyanogen bromide digestion products which bind to 16S rRNA.

The composition of an unusual precursor of 50 S ribosomes in a mutant of Escherichia coli

Escherichia coli strain 15--28 is a mutant which during exponential growth contains large amounts of a '47S' ribonucleoprotein precursor to 50S ribosomes. The '47S particles' are more sensitive to ribonuclease than are 50S ribosomes. The 23 S RNA of 47S particles may be slightly undermethylated, but cannot be distinguished from the 23S RNA of 50S ribosomes by sedimentation or electrophoresis. Isolated particles have 10--15% less protein than do 50S ribosomes; proteins L16, L28 and L33 are absent. Comparison with precursor particles studied by other workers in wild-type strains of E. coli suggests that the assembly of 50S ribosomes in strain 15--28 is atypical.

Effect of arginine on the stability and size of argECBH messenger ribonucleic acid in Escherichia coli

The chemical stability of argECBH messenger ribonucleic acid (mRNA) produced by Escherichia coli was found to be unaltered during steady-state repression by arginine. During extreme arginine deprivation, the increase in argECBH mRNA stability was related to general effects of amino acid starvation on mRNA stability. Thus a mechanism whereby argECBH gene expression is regulated by altering the decay rate of this mRNA is not consistent with our data. Sucrose gradient analysis followed by hybridization revealed that both heavy (14S) and light (8S) components of argECBH mRNA were produced by cells of E. coli K-12 grown without arginine, whereas predominantly light (8S) mRNA was produced by cells grown with arginine. A functional argR gene and the EC portion of the argECBH cluster were found essential for the arginine restriction of heavy-mRNA production. Experiments suggest that light argECBH mRNA did not arise from heavy message, and 8u% of both light and heavy mRNA was found bound to ribosomes. The data appear most consistent with the notion that a second site of control by arginine regulates the amounts of light and heavy arginine mRNA in the cell either by early termination of transcription or by endonucleolytic processing. Consideration of these data in conjunction with those of the accompanying report (Krzyzek and Rogers, 1976) permits the tentative conclusion that light argECBH mRNA is not translated into active enzymes and is thus responsible for the discrepancy between the high content of hybridizable mRNA and low rates of enzyme synthesis found during arginine repression.

A ribonucleoprotein precursor of both the 30S and 50S ribosomal sunbunits of Escherichia coli

A ribonucleoprotein particle (46S) has been isolated from [3H]uridine pulse-labeled cultures of E. Coli AB301/105. Evidence from pulse chase experiments and from protein analysis suggested that this particle may give rise to both the 30S and 50S ribosomal subunits. Direct deproteinization of the particle yielded 30S RNA, while deproteinization after treatment with a crude RNase III preparation yielded products similar to 23S and 16S RNA. This result is consistent with the idea that the 46S ribonucleoprotein is the in vivo counterpart of 30S RNA, which is the in vitro product obtained after phenol extraction.

[Precursors of chloroplast ribosomal RNA and their maturation in Chlorella]

In Chlorella pyrenoidosa, tritiated uridine is incorporated specifically into the RNA of the chloroplast. The 16 S and 23 S ribosomal RNA become labeled after at least 15 min. Short pulse labeling of 5 min results in peaks of radioactivity in the 17 S region and at the heavy side of the 23 S peak, as shown by polyacrylamide electrophoresis.During chase treatment with unlabeled uridine after the pulse labeling, a shift of radioactivity from the 17 S to the 16 S region is observed. At the same time, the radioactivity over the 23 S speak becomes symmetrical. In the 17 S region, there are at least two peaks which appear and disappear during chase treatment. From data of specific radioactivity a precursor-end product relation can be deduced.After blocking of the chloroplast translation with spectinomycin, the RNA in the 17 S region is accumulated. This product is not stringently the same as that from pulse labeling experiments, because it migrates slightly faster than 17 S RNA. Removal of the antibiotic results in a shift of the radioactivity to the 16 S region. At the same time, the previously blocked chloroplast ribosome synthesis is reinitiated.Attempts have been made to localize the precursor molecules of 17 S and 23 S within the cell. By means of differential centrifugation it has been shown that the precursor RNA components are located in ribosomal particles. No free precursor molecules are found in the ribosome-free supernatant. This is the case in normal as well as in spectinomycin-treated cells.The results are discussed in view of the possible role of chloroplast ribosomal particles as processing agents for the maturation of chloroplast ribosomal RNA.

The role of ribonuclease II in the maturation of precursor 16S ribosomal ribonucleic acid in Escherichia coli

The suggested involvement of ribonuclease II in the maturation of rRNA has been examined directly by determining the activity of the enzyme and the amount of p16S rRNA in cell-free extracts from Escherichia coli A19 and its temperature-sensitive derivative N464 grown under experimental conditions designed to vary the amounts of enzyme and precursor independently. In strain A19 the enzyme showed maximum activity in circumstances where the amount of p16S rRNA was normal (e.g. exponential-phase cells) or raised eight times (e.g. during inhibition of growth by methionine starvation of the relaxed auxotroph or by chloramphenicol or puromycin treatment). In strain N464 at the non-permissive temperature the ribonuclease II activity may be decreased by 50% without effect upon the amount of p16S rRNA, whereas in methionine starvation of this strain the enzyme activity is at a maximum and the p16S rRNA is eight times that in exponential-phase cells. These observations are discussed in relation to the previously implied role of ribonuclease II in the maturation of rRNA within ribosome precursors.

Novel ribonucleic acid species accumulated in the dark in the blue-green alga Anacystis nidulans

In the dark, the obligately photoautotrophic blue-green alga Anacystis nidulans accumulates large relative amounts of two novel stable ribonucleic acid species (RNAs). These species are also made in illuminated cells but are unstable in them. When darkened cells are reilluminated, these RNAs are rapidly degraded; degradation is inhibited by chloramphenicol. Upon denaturation with heat or urea, one novel species (0.33 x 10(6) daltons) dissociates into two fragments that comigrate with the second novel species (0.16 x 10(6) daltons) on polyacrylamide gels. Both RNAs are associated with particles sedimenting between 30S and 50S through sucrose gradients and are removed from these particles at low magnesium concentration. The function(s) of these RNAs remains unknown.

Precursor of 5S ribosomal ribonucleic acid in the blue-green alga Anacystis nidulans

The maturation of 5S ribosomal ribonucleic acid (rRNA) in the obligately photoautotrophic unicellular blue-green alga Anacystis nidulans has been studied by using polyacrylamide gel electrophoresis and T1 ribonuclease oligonucleotide analysis. A. nidulans mature 5S rRNA (m5) is of approximately the same molecular weight as the 5S rRNA of Escherichia coli, and is derived by cleavage of a precursor (p5) containing a few (three to six) additional nucleotides. Some of these additional nucleotides occur at the 5' end of the precursor molecule; others may occur at the 3' end. Kinetic experiments indicate that precursors of mature 5S rRNA larger than p5 either do not exist or are very transient in A. nidulans. These results are discussed in relation to those obtained with other prokaryotes.

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.

Observations on the post-transcriptionally modified nucleotides in the 16S ribosomal ribonucleic acid

The 16S (18S) ribosomal ribonucleic acids from a number of organisms were screened for the presence of (some of) the post-transcriptionally modified oligomers found in Escherichia coli 16S ribosomal ribonucleic acid. All prokaryotic 16S species contained all of the modified oligomers tested, with the sole exception that one such oligomer was missing in Alcaligenes faecalis. The post-transcriptional modifications in all of these oligomers except one appear to occur at the later stagesin ribosomal maturation.

Ribosomal ribonucleic acid synthesis and maturation in the blue-green alga Anacystis nidulans

Methods are described for preparation of pulse-labeled ribonucleic acid (RNA) from the blue-green alga Anacystis nidulans. Synthesis of labeled RNA was found to be in part dependent on concurrent photosynthesis and was inhibited by the antibiotic streptolydigin. Mature 23S ribosomal RNA (rRNA) appeared before mature 16S rRNA. Formation of either molecule was inhibited by chloramphenicol, and RNA species of lesser mobility accumulated. These species may be precursors of the mature forms. Maturation of 16S rRNA was also inhibited by streptolydigin. (The effect of this antibiotic on 23S rRNA maturation was not examined). In many respects, ribosomal RNA synthesis and maturation in this blue-green alga appear to follow the pattern already established for bacteria.

Ribonucleic acid synthesis in bacteria treated with toluene

Escherichia coli and Bacillus megaterium rendered permeable to ribonucleoside triphosphates by toluene treatment retain the capacity to synthesize discrete ribonucleic acid species.

The control of ribonucleic acid synthesis in bacteria. The synthesis and stability of ribonucleic acid in chloramphenicol-inhibited cultures of Escherichia coli

The rate of polymerization of ribosomal ribonucleic acid chains was estimated for steadily growing cultures of Escherichia coli M.R.E.600, from the kinetics of incorporation of exogenous [5-(3)H]uracil into completed 23S rRNA molecules. The analytical method of Avery & Midgley (1971) was used. Measurements were made at 37 degrees C, in the presence or the absence of chloramphenicol, in each of three media; enriched broth, glucose-salts or sodium lactate-salts. The rate of chain elongation of 23S rRNA was virtually constant in all media at 37 degrees C, as 24+/-4 nucleotides added/s. Accelerations in the rate of biosynthesis of rRNA by chloramphenicol in growth-limiting media are due primarily to an increase in the rate of initiation of new RNA chains, up to the rates existing in cultures growing rapidly in broth. Thus, in poorer media, only a small fraction of the available DNA-dependent RNA polymerase molecules are active at any given instant, since the chain-initiation rate is limiting in these conditions. In cultures growing rapidly in enriched broth, antibiotic inhibition caused a rise of some 12% in the rate of incorporation of exogenous uracil into total RNA. This small acceleration was due entirely to the partial stabilization of the mRNA fraction, which accumulated as 14% of the RNA formed after the addition of chloramphenicol. In cultures growing more slowly in glucose-salts or lactate-salts media, chloramphenicol caused an immediate acceleration of two- to three-fold in the overall rate of RNA synthesis. Studies by DNA-RNA hybridization showed that the synthesis of mRNA was accelerated in harmony with the other affected species. However, just over half the mRNA formed after the addition of chloramphenicol quickly decayed to acid-soluble products, whereas the remainder was more stable and accumulated in the cells. The mRNA fraction constituted about 6% of the total cellular RNA after 3h inhibition. A model was suggested to explain the partial stabilization and accumulation of the mRNA fraction and the acceleration in the rate of synthesis of mRNA when chloramphenicol was added to cultures in growth-limiting media.

Ribosomal ribonucleic acid synthesis in Bacillus subtilis

The mode of biosynthesis of the 16S and 23S ribosomal ribonucleic acids (rRNA) was studied in Bacillus subtilis 168thy(-). Three criteria were used to define the characteristics of the rRNA species: (i) the time required at 37 degrees C to synthesize 16S and 23S rRNA chains de novo in growing cultures; (ii) the degree of reactivity of the 3'-terminal groups of the rRNA molecules with periodate and [carbonyl-(14)C]isonicotinic acid hydrazide; and (iii) the reactivity of the 5'-terminal regions of the rRNA molecules with the bacterial exonuclease purified by Riley (1969). The 16S and 23S chains of B. subtilis were synthesized at rates of 22+/-2 and 21+/-2 nucleotides added/s. The periodate-[(14)C]isonicotinic acid hydrazide and the exonuclease techniques for estimating apparent chain lengths of RNA indicated that the chain length of the 23S rRNA was 1.8 times that of the 16S fraction. The apparent chain lengths of each rRNA species were: 16S rRNA, 1650+/-50 nucleotide residues; 23S rRNA, 3050+/-90 nucleotide residues. It appears that, the 16S and 23S rRNA molecules in B. subtilis are synthesized in the expected manner, by simple polymerization of the final products on independent cistrons.

Division cycle of Myxococcus xanthus. II. Kinetics of stable and unstable ribonucleic acid synthesis

The kinetics of stable and unstable ribonucleic acid (RNA) synthesis during the division cycle of Myxococcus xanthus growing in a defined medium was determined. Under these conditions, M. xanthus contains one chromosome which is replicated during 80% of the cell cycle. Stable RNA synthesis was measured by pulselabeling an exponential-phase culture with radioactive uridine and then preparing the cells for quantitative autoradiography. By measuring the size of individual cells as well as the number of grains, the rate of stable RNA synthesis as a function of cell size was determined. Unstable RNA synthesis during the division cycle was determined by correlating the data for stable RNA synthesis with the relative amounts of stable and unstable RNA labeled during the short pulse. The data reported here demonstrate that: (i) cells synthesize both stable and unstable RNA throughout the division cycle; (ii) the rate of stable RNA synthesis increases in two discrete steps, corresponding to average ages of 0.15 and 0.75 generations; (iii) the rate of unstable RNA synthesis exhibits an initial rise, followed by a relatively constant rate of synthesis, and finally, a burst of unstable RNA synthesis prior to septum formation. The half-life of unstable RNA of M. xanthus, generation time of 390 min at 30 C, was 4 min. Comparison of the rates of stable and unstable RNA synthesis indicates noncoordinate RNA synthesis within the normal division cycle.

Gene dosage for 5S ribosomal ribonucleic acid in Escherichia coli ad Bacillus megaterium

The number of gene copies for 5S ribosomal ribonucleic acid (rRNA), relative to that for 16 and 23S rRNA, has been determined by deoxyribonucleic acid (DNA)-RNA hybridization for Escherichia coli and Bacillus megaterium. In both cases, the number of 5S rRNA genes equals the number of 16 or 23S rRNA genes. Rapid procedures for preparing extremely highly purified DNA suitable for DNA-RNA hybridization experiments and chemically pure 5S rRNA are described.