Occurrence in vivo of "hidden breaks" at specific sites of 26 S ribosomal RNA of Musca carnaria

Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers

In some eukaryotes, a 'hidden break' has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.), but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although it has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and, in three of these, the break is located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28S rRNA and will be consistently underestimated in the great majority of animal species with a break.

Identification of an Alternative rRNA Post-transcriptional Maturation of 26S rRNA in the Kingdom Fungi

Despite of the integrity of their RNA, some desert truffles present a non-canonical profile of rRNA where 3.3 kb is absent, 1.8 kb is clear and a band of 1.6 kb is observed. A similar rRNA profile was identified in organisms belonging to different life kingdoms, with the exception of the Kingdom Fungi, as a result of a split LSU rRNA called hidden gap. rRNA profiles of desert truffles were analyzed to verify the presence of the non-canonical profile. The RNA of desert truffles and yeast were blotted and hybridized with probes complementary to LSU extremes. RACE of LSU rRNA was carried out to determine the LSU rRNA breakage point. LSU rRNA of desert truffles presents a post-transcriptional cleavage of five nucleotides that generates a hidden gap located in domain D7. LSU splits into two molecules of 1.6 and 1.8 kb. Similar to other organisms, a UAAU tract, downstream of the breakage point, was identified. Phylogenetic comparison suggests that during fungi evolution mutations were introduced in the hypervariable D7 domain, resulting in a sequence that is specifically post-transcriptionally cleaved in some desert truffles.

Molecular characterization of gap region in 28S rRNA molecules in brine shrimp Artemia parthenogenetica and planarian Dugesia japonica

In most insects and some other protostomes, a small stretch of nucleotides can be removed from mature 28S rRNA molecules, which could create two 28S rRNA subunits (28Sα and 28Sβ). Thus, during electrophoresis, the rRNA profiles of these organisms may differ significantly from the standard benchmark since the two subunits co-migrate with the 18S rRNA. To understand the structure and mechanism of the atypical 28S rRNA molecule, partial fragments of 28Sα and 28Sβ in brine shrimp Artemia parthenogenetica and planarian Dugesia japonica were cloned using a modified technology based on terminal transferase. Alignment with the corresponding sequences of 28S rDNAs indicates that there are 41 nucleotides in A. parthenogenetica and 42 nucleotides in D. japonica absent from the mature rRNAs. The AU content of the gap sequences of D. japonica and A. parthenogenetica is high. Both the gaps may form stem-loop structure. In D. japonica a UAAU cleavage signal is identified in the loop, but it is absent in A. parthenogenetica. Thus, it is proposed that the gap processing of 28S rRNA was a late enzyme-dependent cleavage event in the rRNA maturational process based on the AU rich gap sequence and the formation of the stem-loop structure to expose the processing segment, while the deletion of the gap region would not affect the structure and function of the 28S rRNA molecule.

Evaluation of reference genes for real-time PCR quantification of gene expression in the Australian sheep blowfly, Lucilia cuprina

The Australian sheep blowfly, Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae), is an important pest of sheep in Australia and other parts of the world. However, the paucity of information on many fundamental molecular aspects of this species limits the ability to exploit functional genomics techniques for the discovery of new drug targets for its control. The present study aimed to facilitate gene expression studies in this species by identifying the most suitable reference genes for normalization of mRNA expression data. Quantitative real-time polymerase chain reaction (PCR) was performed with 11 genes across RNA samples from eggs, L1, L3, pupae and adult life stages, and two normalization programs, Normfinder and geNorm, were then applied to the data. The results showed an ideal set of genes (18S rRNA, 28S rRNA, GST1, beta-tubulin and RPLPO) for data normalization across all life stages. The most suitable reference genes for studies within specific life stages were also identified. GAPDH was shown to be a poor reference gene. The reference gene recommendations in this study will be of use to laboratories investigating gene expression in L. cuprina and related blowfly species.

Heterologous rRNA gene expression: internal fragmentation of Sciara coprophila 28S rRNA within microinjected Xenopus laevis oocytes

Species-specific pre-rRNA processing variations may result in fragmented 18S, 5.8S and 28S rRNAs. Some insect 5.8S and 28S rRNAs are further cleaved, creating within a 'hidden break' or 'gap'. We investigated the specificity of the processing mechanism by microinjecting Sciara coprophila (fungus fly) rDNA into Xenopus laevis oocytes to examine insect rRNA maturation within a cell where endogenous rRNAs are not cleaved at homologous sites. Results confirm insect rDNA transcription and pre-28S rRNA fragmentation, demonstrating that fly-specific processing machinery is not required. Instead, oocytes may provide required accessory factors, suggesting that the insect gap processing mechanism is served by an evolutionarily conserved apparatus. Alternatively, these results may suggest that processing in some lineages is an autocatalytic property of the rRNA.

Novel processing in a mammalian nuclear 28S pre-rRNA: tissue-specific elimination of an 'intron' bearing a hidden break site

Splitting and apparent splicing of ribosomal RNA, both previously unknown in vertebrates, were found in rodents of the genus Ctenomys. Instead of being formed by a single molecule of 4.4 kb, 28S rRNA is split in two molecules of 2.6 and 1.8 kb. A hidden break, mapping within a 106 bp 'intron' located in the D6 divergent region, is expressed in mature ribosomes of liver, lung, heart and spleen, as well as in primary fibroblast cultures. Testis-specific processing eliminates the intron and concomitantly the break site, producing non-split 28S rRNA molecules exclusively in this organ. The intron is flanked by two 9 bp direct repeats, revealing the acquisition by insertion of a novel rRNA processing strategy in the evolution of higher organisms.

The identification and characterization of a break within the large subunit ribosomal RNA of Trichinella spiralis: comparison of gap sequences within the genus

A break was identified in the large subunit ribosomal RNA of Trichinella spiralis that results in its dissociation into 2 smaller fragments of approximately equal length. The approximate location of the break within the encoding gene was mapped from subcloned rDNA fragments by S1 protection experiments. The boundaries of the break were determined by cDNA primer extension and S1 nuclease protection assays. The excised fragment (gap sequence) was localized to expansion segment 5 within domain IV from which 86 bases are removed during the excision process. The gap region is flanked by the consensus sequence CGAAAG; however, comparison of expansion segment 5 sequences from T. spiralis, T. nativa, T. nelsoni and T. pseudospiralis, all of which undergo 'gap processing', demonstrates significant size and sequence heterogeneity and provides little evidence for additional consensus sequences which could be implicated in gap processing.

Characterization of a 54-nucleotide gap region in the 28S rRNA gene of Schistosoma mansoni

We have analyzed 572 bp in the 28S rDNA of the human blood fluke Schistosoma mansoni which correspond to expansion segment 5 of domain IV as defined by Clark et al. for the Xenopus laevis 28S rRNA. S1 nuclease mapping and primer extension analysis comparing this region with the mature 28S rRNA indicate that there are 54 nucleotides present in the 28S rDNA which are absent from the mature rRNA. This defines a gap that creates two 28S rRNA subunits (28S alpha and 28S beta). Comparison of the S. mansoni sequence with rDNAs of other organisms which contain gaps in their 28S rRNA shows that the overall features are conserved except that the S. mansoni gap is less A + T-rich. The conserved features include: (1) the location of the gap within the 28S rRNA; (2) the predicted secondary structure of the gap, containing a stem-loop with a UAAU sequence within the loop; and (3) a conserved CGAAAGGG on the 3' side of the gap.

Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to domain VII of other eukaryotic 28S rRNAs

We have localized the six ribosomal RNAs (rRNAs) which encode the 28S rRNA region of Trypanosoma brucei. These six rRNAs include two large rRNAs, 28S alpha (approx. 1840 nt) and 28S beta (approx. 1570 nt), and four small rRNAs of approximate sizes 220, 180, 140 and 70 nt. Three of these four small rRNAs (180, 70 and 140) are found at the 3' end of the 28S rRNAs region. Sequence analysis of this area shows that these three small rRNAs encode Domain VII, the last domain of secondary structure in the 28S rRNAs of eukaryotes. Hybridization of labeled nascent RNA to the cloned repeat unit and S1 nuclease protection analysis of putative precursors show that transcription initiates approximately 1.2 kb upstream of the 18S rRNA and terminates after the last small rRNA (140) at the 3' end of the 28S rRNA region. Analysis of three putative rRNA precursors suggests that the small rRNAs are not processed from the primary transcript until after the usual processing of the 5.8S rRNA region.

rRNA processing: removal of only nineteen bases at the gap between 28S alpha and 28S beta rRNAs in Sciara coprophila

We have determined the sequence of the rDNA region between the 28S alpha and 28S beta rRNA coding segments (termed a "gap") in the insect Sciara coprophila, and have used S1 nuclease mapping and cDNA primer extension to define the 5' and 3' boundaries of the gap. Only 19 bases found in rDNA at the gap region are absent from mature 28S rRNA. Eukaryotic rRNAs contain stretches of nucleotides ("expansion segments") which are absent in E. coli rRNA. The gap region in Sciara is located within expansion segment V. Therefore, the excision of 19 bases in the Sciara gap suggests that a large portion of expansion segment V plays no function in mature ribosomes. Specific sequences conserved in Sciara and Drosophila are considered as candidates for recognition signals for the excision of the gap transcript.

Hidden breaks in ribosomal RNA of phylogenetically tetraploid fish and their possible role in the diploidization process

Hidden breaks occur in the ribosomal RNA of tetraploid Cyprinid fish such that the large ribosomal RNA (28 S) yields upon denaturation two RNA fragments of 8.7 X 10(5) and 5.0 X 10(5) daltons, whereas the small rRNA (18 S) yields fragments of 3.2 X 10(5) to 5.0 X 10(4) daltons. In tetraploid Cyprinids hidden breaks occur only in the rRNA of somatic tissue and not in oocytes and sperm cells. Hidden breaks can be detected only slightly in diploid Cyprinid species. Ribosomes purified from somatic tissue of tetraploid Cyprinids show a reduced efficiency in protein synthesis in vitro. The ribosomal proteins from diploid and tetraploid Cyprinid fish show considerable electrophoretic differences. This is discussed in light of a possible functional role of hidden breaks in rRNA in the process of diploidization of gene expression in tetraploid Cyprinid species.

Size heterogeneity of ribosomal RNA in eukaryote evolution--2. rRNA molecular weights in species containing discontinuous large ribosomal subunit RNA

1. The molecular weights and the integrity of the principal rRNA species derived from the large and small ribosomal subunit (respectively, L-rRNA and S-rRNA) of several species of Protostomia and Protozoa have been investigated. 2. Using gel electrophoresis in formamide, the molecular weights of protostomian L-rRNA species have been found to range from 1.30 X 10(6) (Annelida) to 1.61 X 10(6) (Diptera); those of the S-rRNA's cover the range 0.65 X 10(6) (Annelida)-0.81 X 10(6) (Diptera). 3. Both rRNA components have incurred extensive changes among the Protozoa; the L-rRNA ranges in weight from 1.35 X 10(6) (T. pyriformis) to 1.57 X 10(6) (A. castellanii) and the S-rRNA from 0.70 X 10(6) of T. pyriformis to 0.85 X 10(6) of A. castellanii and E. gracilis. 4. The L-rRNA components of all the species investigated are discontinuous molecules endowed with a latent median break; depending on whether the nick is located at the centre of the L-rRNA chain, or lies off-centre, the molecular weight of the S-rRNA equals that of either both, or only one, of the two fragments composing the L-rRNA.

Sequence arrangement of the rRNA genes of the dipteran Sarcophaga bullata

Velocity sedimentation studies of RNA of Sarcophaga bullata show that the major rRNA species have sedimentation values of 26S and 18S. Analysis of the rRNA under denaturing conditions indicates that there is a hidden break centrally located in the 26S rRNA species. Saturation hybridization studies using total genomic DNA and rRNA show that 0.08% of the nuclear DNA is occupied by rRNA coding sequences and that the average repetition frequency of these coding sequences is approximately 144. The arrangement of the rRNA genes and their spacer sequences on long strands of purified rDNA was determined by the examination of the structure of rRNa:DNA hybrids in the electron microscope. Long DNA strands contain several gene sets (18S + 26S) with one repeat unit containing the following sequences in order given: (a) An 18S gene of length 2.12 kb, (b) an internal transcribed spacer of length 2.01 kb, which contains a short sequence that may code for a 5.8S rRNA, (c) A 26S gene of length 4.06 kb which, in 20% of the cases, contains an intron with an average length of 5.62 kb, and (d) an external spacer of average length of 9.23 kb.

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.

Physicochemical characterization of the ribosomal RNA species of the Mollusca. Molecular weight, integrity and secondary-structure features of the RNA of the large and small ribosomal subunits

1. The rRNA species of the Cephalopoda Octopus vulgaris and Loligo vulgaris were found to have unexpectedly high sedimentation coefficients and molecular weights. In 0.1 M-NaCl the L-rRNA (RNA from large ribosomal subunit) has the same s20 value as the L-rRNA of the mammals (30.7S), whereas the S-rRNA (RNA from small ribosomal subunit) sediments at a faster rate (20.1S) than the S-rRNA of both the mammals and the fungi (Neurospora crassa) (17.5S). The molecular weights of the L-rRNA were determined by gel electrophoresis in formamide and found to be 1.66 X 10(6) (Octupus) and 1.89 X 10(6) (Loligo); the mol.wt. of the S-rRNA of both species is 0.96 X 10(6), i.e. much larger than that of the mammals (0.65 X 10(6)) and almost coincident with that of the '23S' RNA of the prokaryotes. 2. By contrast, the less evolved Gastropoda and Lamellibranchiata (Murex trunculus and Macrocallista chione) have S-rRNA and L-rRNA species with mol.wts. of 0.65 X 10(6) and approx. 1.40 X 10(6).3. All the mature L-rRNA molecules of the cephalopoda are composed of two unequal fragments held together by regions of hydrogen-bonding having a similar, low, thermal stability in the two species; the molecular weights of the two fragments composing the L-rRNA are estimated to be 0.96 X 10(6) and 0.88 X 10(6) (Loligo) and 0.96 X 10(6) and 0.65 X 10(6) (Octupus). THe S-rRNA of both species is a continuous chain with exactly the same molecular weight (0.96 X 10(6)) as the heavier of the two fragments of the L-rRNA. 4. The secondary-structure features of the L-rRNA and S-rRNA species of the Caphalopoda were investigated by thermal 'melting' analysis in 4.0 M-guanidinium chloride; 60-70% of the residues are estimated to form short, independently 'melting' bihelical segments not more than 10 base-pairs in length. 5. Bases are unevenly distributed between non-helical and bihelical portions of the rRNA molecules, G and C residues being preferentially concentrated in bihelical comains. 6. The secondary-structure regions of the L-rRNA species of Octopus and Loligo are heterogenous, including two discrete fractions of independently 'melting' species that give rise to biphasic 'melting' profiles: a fraction consisting of shorter (G + C)-poorer segments (60-68% G + C, not more than 5 base-pairs in length) and a fraction consisting of longer (G + C)-richer segments (80-88% G + C, 5-10 base-pairs in length). No evidence for heterogeneity has been detected in the S-rRNa.

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.

Introduction of hidden breaks during rRNA maturation and ageing in Tetrahymena pyriformis

The stability of Tetrahymena pyriformis cytoplasmic rRNAs and nuclear rRNA precursors has been studied by polyacrylamide gel electrophoresis under partly and completely denaturing conditions. Cytoplasmic 17-S rRNA (Mr = 0.66 X 10(6) consists of a continuous polynucleotide chain throughout its lifetime, whereas the bulk of 26-S rRNA (Mr = 1.2m X 10(6) dissociates upon denaturation. Two large fragments (F1, F2) of somewhat different molecular weights (Mr 0.63 X 10(6) and 0.58 X 10(6) and the small 5.8-S rRNA fragment (Mr about 50 000) are regularly observed. Some additional distinct minor fragments (F3-F6) are noted under certain preparative conditions, suggestive of artifactual origin. The following conclusions were made from the data obtained . (a) Newly synthesized 26-S rRNA molecules do not contain the 'central' hidden break (separating F1 and F2) until about 15 min after their appearance in the cytoplasm; however, they release during denaturation the 5.8-S and/or a short-lived 7-S fragment (Mr about 75 000) which might represent a direct precursor to the 5.8-S rRNA. (b) The immediate nuclear precursor to the 26-S rRNA (Mr 1.39 X 10(6) releases a small fragment of similar size (7 S). (c) The largest stable transcription product of the rDNA (pre-rRNA) does not contain any hidden break.

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.