Studies of the thermal conversion of 28 S RNA of Galleria mellonella (L.) to an 18 S product

Comparison of five commercial kits for isolation of total RNA in samples of WSSV-infected shrimp

Viral diseases are the most serious threat to the expansion and development of shrimp aquaculture. Rapid diagnosis of the white spot syndrome virus (WSSV), a lethal shrimp pathogen, is essential to restrict its spread and reduce the mortality of infected shrimp. This virus has globally affected the shrimp farming industry, with a devastating economic impact. Several studies have focused on the expression of WSSV transcripts to understand the molecular mechanisms governing the pathological development of the disease. Since gene expression studies and molecular diagnostics at the early stages of infection depend on the efficient isolation of high-quality RNA, the extraction methods should be carefully selected. However, previous comparisons of the performance of RNA isolation kits have yet to be systematically investigated. In this study, 5 commercial RNA extraction methods were compared in WSSV-infected shrimp. The highest total RNA yield (ng mg-1 tissue) was obtained using TRIzol. Even though the 260/280 nm absorption ratios showed significant differences, the methods showed good purity values (>2.0). RNA integrity was evaluated in a denaturing agarose gel electrophoresis, and degradation was observed after the total RNA samples were treated with DNase I. Finally, the method that allowed the earlier detection of WSSV transcripts by qRT-PCR was the Zymo Direct-zol RNA MiniPrep kit. This study shows that the amount of observed (or estimated) WSSV transcripts might be affected because of the RNA isolation method. In addition, these results may contribute to improve the accuracy of the results obtained in gene expression studies, for more sensitive and robust detection of WSSV.

Ammonia transporter 2 as a molecular marker to elucidate the potentials of ammonia transport in phylotypes of Symbiodinium, Cladocopium and Durusdinium in the fluted giant clam, Tridacna squamosa

Giant clams harbor coccoid Symbiodiniaceae dinoflagellates that are phototrophic. These dinoflagellates generally include multiple phylotypes (species) of Symbiodinium, Cladocopium, and Durusdinium in disparate proportions depending on the environmental conditions. The coccoid symbionts can share photosynthate with the clam host, which in return supply them with nutrients containing inorganic carbon, nitrogen and phosphorus. Symbionts can recycle nitrogen by absorbing and assimilating the endogenous ammonia produced by the host. This study aimed to use the transcript levels of ammonia transporter 2 (AMT2) in Symbiodinium (Symb-AMT2), Cladocopium (Clad-AMT2) and Durusdinium (Duru-AMT2) as molecular indicators to estimate the potential of ammonia transport in these three genera of Symbiodiniaceae dinoflagellates in different organs of the fluted giant clam, Tridacna squamosa, obtained from Vietnam. We also determined the transcript levels of form II ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcII) and nitrate transporter 2 (NRT2) in Symbiodinium (Symb-rbcII; Symb-NRT2), Cladocopium (Clad-rbcII; Clad-NRT2) and Durusdinium (Duru-rbcII; Duru-NRT2), in order to examine the potential of ammonia transport with reference to the potentials of phototrophy or NO₃^- uptake independent of the quantities and proportion of these Symbiodiniaceae phylotypes. Our results indicated for the first time that phylotypes of Symbiodinium and Cladocopium could have different potentials of ammonia transport, and that phylotypes of Symbiodinium might have higher potential of NO₃^- transport than ammonia transport. They also suggested that Symbiodiniaceae phylotypes residing in different organs of T. squamosa could have disparate potentials of ammonia transport, alluding to the functional diversity among phylotypes of coccoid Symbiodinium, Cladocopium, and Durusdinium.

Sticky problems: extraction of nucleic acids from molluscs

Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. DNA extraction methods that employ the detergent hexadecyltrimethylammoniumbromide (CTAB) to remove these contaminants importantly facilitate molecular-level study of molluscs. Molluscan pigments may stain DNA samples and interfere with spectrophotometry, necessitating gel electrophoresis or fluorometry for accurate quantification. RNA can reliably be extracted but the 'hidden break' in 28S rRNA of molluscs (like most protostomes) causes 18S and 28S rRNA fragments to co-migrate electrophoretically. This challenges the standard quality control based on the ratio of 18S and 28S rRNA, developed for deuterostome animals. High-AT content in molluscan rRNA prevents the effective purification of polyadenylated mRNA. Awareness of these matters aids the continuous expansion of molecular malacology, enabling work also with museum specimens and next-generation sequencing, with the latter imposing unprecedented demands on DNA quality. Alternative methods to extract nucleic acids from molluscs are available from literature and, importantly, from communications with others who study the molecular biology of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Regulation of gene expression encoding the digestive α-amylase in the larvae of Colorado potato beetle, Leptinotarsa decemlineata (Say) in response to plant protein extracts

Considering the relevance of insect α-amylases and natural α-amylase inhibitors present in plants to protect against insect damage, we investigated the effect of white bean and rapeseed protein extracts on digestive α-amylase gene expression of the Colorado potato beetle, Leptinotarsa decemlineata (Say). For this purpose, in vitro and in vivo trials were performed to determine the inhibitory activity of seed proteins on the third and fourth instar larvae. In both trials, the significant inhibitory effect of each extracts on the third and fourth instar larval α-amylase activity and considerable mortality in treatments were observed compared to control trials. In the RT-qPCR, expression ratio demonstrated that the α-amylase gene of two different larval stages grown on both proteins treated leaves had significantly differentiated expression and was up-regulated in third instar larvae and down-regulated in fourth instar larvae compared to control. Results suggest that the hyper-production of α-amylase in third instar larvae is elicited to compensate for the enzyme activity inhibition at an earlier stage and also down-regulation suggests the existence of a negative feedback of plant proteins on the last instar larvae via impaired food intake and digestive α-amylase activity in Colorado potato beetle. Therefore, disruption of the insect's digestive physiology by plant defensive proteins can be considered in the development of innovative controlling methods of this crucial potato pest.

RNA profile diversity across arthropoda: guidelines, methodological artifacts, and expected outcomes

High-quality RNA is an important precursor for high-throughput RNA sequencing (RNAseq) and subsequent analyses. However, the primary metric used to assess RNA quality, the RNA Integrity Number (RIN), was developed based on model bacterial and vertebrate organisms. Though the phenomenon is not widely recognized, invertebrate 28S ribosomal RNA (rRNA) is highly prone to a form of denaturation known as gap deletion, in which the subunit collapses into two smaller fragments. In many nonmodel invertebrates, this collapse of the 28S subunit appears as a single band similar in size to the 18S rRNA subunit. This phenomenon is hypothesized to be commonplace among arthropods and is often misinterpreted as a "degraded" rRNA profile. The limited characterization of gap deletion in arthropods, a highly diverse group, as well as other nonmodel invertebrates, often biases RNA quality assessments. To test whether the collapse of 28S is a general pattern or a methodological artifact, we sampled more than half of the major lineages within Arthropoda. We found that the 28S collapse is present in ∼90% of the species sampled. Nevertheless, RNA profiles exhibit considerable diversity with a range of banding patterns. High-throughput RNAseq and subsequent assembly of high-quality transcriptomes from select arthropod species exhibiting collapsed 28S subunits further illustrates the limitations of current RIN proxies in accurately characterizing RNA quality in nonmodel organisms. Furthermore, we show that this form of 28S denaturation, which is often mistaken for true "degradation," can occur at relatively low temperatures.

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.

'Degraded' RNA profiles in Arthropoda and beyond

The requirement for high quality/non-degraded RNA is essential for an array of molecular biology analyses. When analysing the integrity of rRNA from the barnacle Lepas anatifera (Phylum Arthropoda, Subphylum Crustacea), atypical or sub-optimal rRNA profiles that were apparently degraded were observed on a bioanalyser electropherogram. It was subsequently discovered that the rRNA was not degraded, but arose due to a ‘gap deletion’ (also referred to as ‘hidden break’) in the 28S rRNA. An apparent excision at this site caused the 28S rRNA to fragment under heat-denaturing conditions and migrate along with the 18S rRNA, superficially presenting a ‘degraded’ appearance. Examination of the literature showed similar observations in a small number of older studies in insects; however, reading across multiple disciplines suggests that this is a wider issue that occurs across the Animalia and beyond. The current study shows that the 28S rRNA anomaly goes far beyond insects within the Arthropoda and is widespread within this phylum. We confirm that the anomaly is associated with thermal conversion because gap-deletion patterns were observed in heat-denatured samples but not in gels with formaldehyde-denaturing.

Insects' RNA Profiling Reveals Absence of "Hidden Break" in 28S Ribosomal RNA Molecule of Onion Thrips, Thrips tabaci

With an exception of aphids, insects' 28S rRNA is thought to harbor a "hidden break" which cleaves under denaturing conditions to comigrate with 18S rRNA band to exhibit a degraded appearance on native agarose gels. The degraded appearance confounds determination of RNA integrity in laboratories that rely on gel electrophoresis. To provide guidelines for RNA profiles, RNA from five major insect orders, namely, Diptera, Hemiptera, Thysanoptera, Hymenoptera, and Lepidoptera, was compared under denaturing and nondenaturing conditions. This study confirmed that although present in most of insect's RNA, the "hidden break" is absent in the 28S rRNA of onion thrips, Thrips tabaci. On the other hand, presence of "hidden break" was depicted in whiteflies' 28S rRNA despite their evolutionary grouping under same order with aphids. Divergence of 28S rRNA sequences confirms variation of both size and composition of gap region among insect species. However, phylogeny reconstruction does not support speciation as a possible source of the hidden break in insect's 28S rRNA. In conclusion, we show that RNA from a given insect order does not conform to a particular banding profile and therefore this approach cannot be reliably used to characterize newly discovered species.

Comparison of RNA isolation methods from insect larvae

Isolating RNA from insects is becoming increasingly important in molecular entomology. Four methods including three commercial kits RNeasy Mini Kit (Qiagen), SV Total RNA isolation system (Promega), TRIzol reagent (Invitrogen), and a cetyl trimethylammonium bromide (CTAB)-based method were compared regarding their ability to isolate RNA from whole-body larvae of Thaumatotibia leucotreta (Meyrick), Thanatophilus micans (F.), Plutella xylostella (L.), and Tenebrio molitor (L.). A difference was observed among the four methods regarding RNA quality but not quantity. However, RNA quality and quantity obtained was not dependent on the insect species. The CTAB-based method produced low-quality RNA and the Trizol reagent produced partially degraded RNA, whereas the RNeasy Mini Kit and SV Total RNA isolation system produced RNA of consistently high quality. However, after reverse transcription to cDNA, RNA produced using all four extraction methods could be used to successfully amplify a 708 bp fragment of the cytochrome oxidase I gene. Of the four methods, the SV Total RNA isolation system showed the least amount of DNA contamination with the highest RNA integrity number and is thus recommended for stringent applications where high-quality RNA is required. This is the first comparison of RNA isolation methods among different insect species and the first to compare RNA isolation methods in insects in the last 20 years.

Fasciola hepatica - where is 28S ribosomal RNA?

Advanced molecular biology techniques are currently used to develop new effective strategies against fasciolosis. Assessment of the quality of extracted total RNA is an important step prior to commencing many molecular biology methods such as transcriptomics. However, RNA quality assessment is complicated for some organisms, including Fasciola hepatica, by the absence of a 28S rRNA peak/band, when assessed with modern protocols. In this study, electrophoretic profiles of F. hepatica ribosomal RNAs were evaluated using microfluidics capillary based and conventional non-denaturing gel electrophoresis methods. An important modification to recommended protocols, the exclusion of heat-denaturation step, in the microfluidics capillary based electrophoresis is critical to visualise the expected 28S rRNA and obtain an RNA integrity number (RIN). The intensity of the 28S rRNA band is reduced by the effect of non-denaturing gel electrophoresis.

Degradation of rRNA in BM-N cells from the silkworm Bombyx mori during abortive infection with heterologous nucleopolyhedroviruses

Cell lines derived from the silkworm, Bombyx mori, are only permissive for B. mori nucleopolyhedrovirus (NPV), with other NPVs generally resulting in abortive infection. Here, we demonstrate that rRNA of B. mori BM-N cells undergoes rapid degradation through site-specific cleavage upon infection with NPVs from Autographa californica (AcMNPV), Hyphantria cunea (HycuMNPV), Spodoptera exigua (SeMNPV) and Spodoptera litura (SpltMNPV). No significant decreases in cellular RNA were observed in Ld652Y, Se301, Sf9, SpIm and S2 cells infected with AcMNPV or HycuMNPV, indicating the response is unique to BM-N cells. A transient expression assay using a cosmid library of the HycuMNPV genome demonstrated that HycuMNPV P143 is responsible for rRNA degradation, which was also detected in BM-N cells transfected with plasmids expressing the P143 proteins from AcMNPV, SeMNPV and SpltMNPV. These results indicate that B. mori evolved to acquire a unique antiviral immune mechanism that is activated by P143 proteins from heterologous NPVs.

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.

MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits

Background

Describing and evaluating miRNA inventories with Next Generation Sequencing is a goal of scientists from a wide range of fields. It requires high purity, high quality, and high yield RNA extractions that do not only contain abundant ribosomal RNAs but are also enriched in miRNAs. Here we compare 6 disparate and commercially available totalRNA extraction kits for their suitability for miRNA-preparations from Gyrodactylus salaris, an important but small (500 μm in length) monogenean pathogen of Norwegian Atlantic salmon (Salmo salar).

Findings

We evaluated 1 salt precipitation method (MasterPure™ Complete RNA Purification Kit, Epicentre), 2 Phenol based extraction methods (mirVana Kit, Ambion, and Trizol Plus Kit, Invitrogen), 1 paramagnetic bead extraction method (RNA Tissue kit, GeneMole) and 2 purification methods based on spin column chromatography using a proprietary resin as separation matrix (Phenol-free Total RNA Purification Kit, Amresco, and ZR MicroPrep Kit, Zymo Research). The quality of the extractions from 1, 10 and 100 individuals, respectively, was assessed in terms of totalRNA yield, RNA integrity, and smallRNA and miRNA yield. The 6 RNA extraction methods yielded considerably different total RNA extracts, with striking differences in low molecular weight RNA yield. The Phenol-free Total RNA Purification Kit (Amresco) showed the highest totalRNA yield, but the best miRNA/totalRNA ratio was obtained with the ZR MicroPrep Kit (Zymo Research). It was not possible to extract electrophoretically detectable miRNAs from Gyrodactylus salaris with the RNA Tissue Kit (GeneMole) or the Trizol Plus Kit (Invitrogen).

Conclusions

We present an optimized extraction protocol for single and small numbers of Gyrodactylus salaris from infected Atlantic salmon that delivers a totalRNA yield suitable for downstream next generation sequencing analyses of miRNA. Two of the six tested totalRNA kits/methods were not suitable for the extraction of miRNAs from Gyrodactylus salaris.

Why does insect RNA look degraded?

The integrity of extracted ribonucleic acid (RNA) is commonly assessed by gel electrophoresis and subsequent analysis of the ribosomal RNA (rRNA) bands. Using the honey bee, Apis mellifera (Hymenoptera: Apidae), as an example, the electrophoretic rRNA profile of insects is explained. This profile differs significantly from the standard benchmark since the 28S rRNA of most insects contains an endogenous "hidden break." Upon denaturation, the masking hydrogen bonds are disrupted, releasing two similar sized fragments that both migrate closely with 18S rRNA. The resulting rRNA profile thus reflects the endogenous composition of insect rRNA and should not be misinterpreted as degradation.

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.

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.

Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.

Analysis of two D1-like dopamine receptors from the honey bee Apis mellifera reveals agonist-independent activity

Dopamine is found in many invertebrate organisms, including insects, however, the mechanisms through which this amine operates remain unclear. We have expressed two dopamine receptors cloned from honey bee (AmDOP1 and AmDOP2) in insect cells (Spodoptera frugiperda), and compared their pharmacology directly using production of cAMP as a functional assay. In each assay, AmDOP1 receptors required lower concentrations of dopamine and 6,7-ADTN for maximal activation than AmDOP2 receptors. Conversely, butaclamol and cis(Z)-flupentixol were more potent at blocking the cAMP response mediated through AmDOP2 than AmDOP1 receptors. Expression of AmDOP1, but not AmDOP2, receptors significantly increased levels of cAMP even in the absence of ligand. This constitutive activity was blocked by cis(Z)-flupentixol. This work provides the first evidence of a constitutively activated dopamine receptor in invertebrates and suggests that although AmDOP1 and AmDOP2 share much less homology than their vertebrate counterparts, they display a number of functional parallels with the mammalian D1-like dopamine receptors.

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.

Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid: implication for diversification of insect rRNA

Determination of the entire nucleotide sequence of the aphid 28S ribosomal RNA gene (28S rDNA) revealed that it is 4,147 bp in length with a G + C content of 60.3%. Based on the nucleotide sequence, we constructed a presumed secondary-structure model of the aphid 28S rRNA which indicated that the aphid 28S rRNA is characterized by the length and high G + C content of its variable regions. The G + C content of the aphid's variable regions was much higher than that of the entire sequence of the 28S rRNA, which formed a striking contrast to those of Drosophila with the G + C content much lower than the entire 28S molecule. In this respect, the aphid 28S rRNA somewhat resembled those of vertebrates. This is the third report of a complete large-subunit rRNA sequence from an arthropod, and the first 28S rRNA sequence for a nondipterous insect.

Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure

We report the sequence and propose a secondary structure for the cytoplasmic large subunit (5.8S and 28S) ribosomal RNA of the mosquito, Aedes albopictus, in an aligned format that incorporates secondary structure comparisons with Homo sapiens, Drosophila melanogaster, and Escherichia coli ribosomal RNAs. This format facilitates comparison of subtle differences between models, allowing nucleotide by nucleotide analysis at each position of discrepancy. Comparison of the A. albopictus large subunit ribosomal RNA gene with those from other species revealed new compensatory base changes. The aligned format focuses attention to the specific contribution of the A. albopictus sequence by facilitating comparison with the sequence of another dipteran, D. melanogaster. This is the second report of a complete large subunit rRNA sequence from an arthropod, and the first 28S rRNA sequence for a member of the lower Diptera (Nematocera).

What causes the aphid 28S rRNA to lack the hidden break?

In order to determine why the aphid 28S rRNA lacks the hidden break otherwise found in insects, the structure of the region of the aphid ribosomal DNA (rDNA) corresponding to the gap region, which in other insect rDNA transcripts is excised posttranscriptionally, was studied. Sequence comparison suggested that, in contradistinction to what is found in rDNA transcripts of other insects, a stem-loop structure formed in this region of the aphid rDNA transcript is not AU-rich. Nor did the loop of the aphid molecule contain the UAAU tract that can be a signal for the introduction of the hidden break, suggesting that in this particular region the aphid 28S rRNA resembles 28S rRNAs of deuterostomes, which do not contain the hidden break.

Giardia intestinalis antigens expressed in Escherichia coli

cDNA and genomic DNA of Giardia intestinalis have been cloned in pUC vectors and used to express Giardia antigens in Escherichia coli. Several expression libraries have been produced and positive clones identified by immuno-colony assays with antisera raised against whole parasites and partially purified antigen(s). Those clones which express G. intestinalis antigens have been used to raise antisera in mice and the antisera used in immunofluorescence assays. The proteins expressed by the clones have been shown to represent a 32 kDa protein of the flagellae and axonemes, a protein associated with the spiral part of the ventral disc, proteins covering the surface of the trophozoite or associated with the coat, and other proteins associated with axonemes of posterolateral flagellae, kinetosomes and funis, and the anterolateral axonemes. mRNA was purified from G. intestinalis and translated in a cell free lysate. A rabbit antiserum raised against trophozoites immunoprecipitated several translation products while an antiserum raised against a purified 32 kDa protein only immunoprecipitated this protein. G. intestinalis rRNA subunits also were examined in the course of mRNA purification. Two rRNA species were evident, the small rRNA and the post-transcriptionally processed large rRNA.

Molecular mechanism of introduction of the hidden break into the 28S rRNA of insects: implication based on structural studies

We determined the structure around the gap region between 28S alpha and 28S beta rRNA of Bombyx mori, a lepidopteran insect, to know the introduction mechanism of the hidden break, an interruption of the phosphodiester bond specific to the 28S rRNA of protostomes. Sequence analysis and S1 nuclease mapping suggested that a stretch of 30 nucleotides is excised from the mid region of the 28S rRNA to generate the hidden break. The length of excluded stretch was very various among three insects so far studied. However, the gap responsible for the hidden break was located in a fixed position in the 28S rRNA irrespective of insect species. It was suggested that extremely AU-rich sequence including the specific UAAU tract forming a loop can be a signal for the introduction of the hidden break. The same signal seemed also involved in splitting the dipteran 5.8S rRNA.

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.

Nucleotide sequence and thermal property of 5S rRNA from the elder aphid. Acyrthosiphon magnoliae

The nucleotide sequence of 5S rRNA from the elder aphid. Acyrthosiphon magnoliae was determined by using postlabeling sequencing techniques. The aphid 5S rRNA consists of 120 nucleotides and the sequence differs from those of Bombyx and Drosophila 5S rRNAs in 14 and 16 positions, respectively. A secondary structure model based on the sequence has two distinctive features : the helix I is shorter and the total free energy lower. Judging from the thermal profile, the aphid 5S rRNA likely assumes a conformation somewhat different from those of the other two insects.

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.

Trypanosoma cruzi ribosomal RNA: internal break in the large-molecular-mass species and number of genes

The large-molecular-mass ribosomal ribonucleic acid from Trypanosoma cruzi probably contains an internal break. The molecule can be obtained in its intact form or in its two fragments depending on the denaturing agents used for its purification and/or display. This break appears to be an in vivo late processing step rather than a random nucleolytic cleavage during in vitro manipulations. Calculations of mass, from gel electrophoretograms, for the large and small main ribosomal ribonucleic acid species and for the two chains derived from the large species gave values of 1.37, 0.84, 0.70 and 0.57 X 10(6) daltons, respectively. Sedimentation velocity measurements in sucrose gradients and in the analytical ultracentrifuge indicated sedimentation coefficients of 24 and 18 S for the large and small main species, respectively. Saturation hybridization curves showed that the nuclear genome, quantified by chemical analysis, contains about 114 ribosomal ribonucleic acid gene copies.

Catfish vitellogenin and its messenger RNA are smaller than their chicken and Xenopus counterparts

Injection of male bullheads (Ameiurus nebulosus) with estradiol induced the production of a major serum phosphoprotein of molecular weight 145,000. This protein was immunoprecipitable by antisera raised against lipovitellin from bullhead eggs and was absent from the serum of control males. Production of this serum protein coincided with changes in the liver mRNA population, which suggested that estradiol had induced the synthesis of additional mRNA sequences in the high-frequency class. Agarose gel electrophoresis in the presence of methyl mercury hydroxide showed that this mRNA population contained at least one species which was not present in the liver of uninjected males. This new RNA was the major polyadenylated species present in the total cellular RNA and its size relative to ribosomal RNAs and locust vitellogenin mRNA was estimated as 5800 nucleotides. When the liver total RNAs were translated in the mRNA-dependent rabbit reticulocyte lysate system the major translation product from the induced fish had the same molecular weight (145,000) as the serum phosphoprotein and was immunoprecipitable by antilipovitellin antisera. This translation product was not coded for by RNA from control fish. These observations are consistent with the induction of vitellogenesis by estradiol as reported in other egg-laying vertebrates and they show that bullhead vitellogenin and its mRNA are significantly smaller than their avian and amphibian counterparts.

The effect of cytosine arabinoside on the synthesis of rapidly labeled RNA during DNA replicating and non-DNA replicating periods of the cell cycle

The effects of various concentrations of cytosine arabinoside (Ara-C) on the rates of DNA and RNA synthesis were investigated during the peak of DNA synthesis, using a naturally synchronized culture of Aedes aegypti (mosquito) cells. During this stage of the cell cycle, the synthesis of both DNA and RNA was found to be progressively inhibited with increasing concentrations of Ara-C. When the same concentrations of Ara-C were added to the culture at a time period when no DNA was being synthesized, it was found that the synthesis of RNA was not inhibited. Rapidly labeled polysomal RNA species were isolated from cultured cells in which DNA was being synthesized. The synthesis of these RNA species is inhibited completely in the presence of a concentration of Ara-C which inhibits 90% of DNA synthesis. It is suggested that during periods of DNA replication, Ara-C is a selective inhibitor of the synthesis of rapidly labeled RNA species or of the processing of these RNA species from the nucleus to the polysomes.

Quantitative data on the Bombyx mori L. silkworm: a review

This paper summarizes a variety of quantitative data on the silkworm Bombyx mori, collected in the literature, to help building models on silk gland differentiation. The properites of the silk gland and their changes especially during the last larval instar have been reviewed (size, DNA, RNA amino acids, enzymes). The components of the silk (fibroin and sericin) are also studied (molecular weight, composition). Thus translation and transcription rates have been estimated. The relevant data on the fat body and the haemolymph are also given, as well as some characteristics of the oocyte/egg system.

Preservation of algal and higher plant ribosomal RNA integrity during extraction and electrophoretic quantitation

Isolation of high molecular weight ribosomal RNA from the wall-less alga Olisthodiscus luteus and the angiospermous plant Sauromatum guttatum is described. It has been found that a buffer which contains magnesium must be used to successfully isolate Olisthodiscus rRNA whereas the isolation of intact Sauromatum rRNA requires a buffer system containing a high amount of the chelator EDTA. Sauromatum but not Olisthodiscus extracts were contaminated with ribonuclease unless the inhibitor diethylpyrocarbonate was used during the ribonucleic acid extraction procedure. Nuclease levels were monitored by coincubating [3H]-labeled Escherichia coli ribosomal RNA with the experimental RNA samples. The effects of detergents on the isolation and quantitation of RNA are presented, and methods to avoid loss of highly thermolabile plant ribosomal RNA species are discussed.

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.

Arthropod ribosomes. Integrity of ribosomal ribonucleic acids from aphids and water fleas

The 28 S aphid rRNA differs from those of the other insects in two points: (1) it lacks the primary nick; (2) it is larger by 0.2 - 106 daltons. The 28 S rRNA from water fleas also, like that from crayfish, is larger than those from comon insects by 0.2 - 106 daltons. These crustacean 28-S rRNAs were shown to contain the primary nick, which is probably not located in the central point. The 18-S rRNAs from aphids and water fleas had molecular weights significantly larger than 0.7 - 106, the common vaalue for the eukaryotic 18 S rRNA. It was was suggested that the 3'-terminal base sequences of these RNAs are different from the common sequences of these RNAs are different from the common sequence proposed for the 18 S rRNAA of eukaryotes. These exceptional characteristics of the rRNAs from the parthenogenetic animals may provide a probe for general functions of the rRNA in the eukaryotic ribosomes.

Conservation of the 5'-terminal nucleotide sequences of ribosomal 18-S RNA in eukaryotes. Differential evolution of large and small ribosomal RNA

The 5'-terminal nucleotide sequences of ribosomal 18-S and 28-S RNA of seven species of eukaryotes including three mammals, one bird, one amphibian, one echinoderm and one slime mold, were analyzed either by means of terminal phosphorylation of RNA with polynucleotide kinase of by fingerprint analysis of uniformly labeled RNA. The following conclusions were obtained. 1. The 5'-terminal sequences of the 18-S RNA of the mouse, chicken and Dictyostelium discoideum were pUpApCp(Cp,Up)Gp---, suggesting strongly that all the eukaryotes had this same sequence at the 5'-terminus. Preliminary analysis of the 5'-termini of the 18-S RNA from human, rat, Xenopus and sea urchin cells revealed the same pUp(Np)Gp--- type 5'-terminal structure, supporting the above hypothesis. 2. The 5'-terminal sequences of the 28-S RNA of the human, rat, mouse and chicken cells were all pCpGp---, whereas those of the lower animals such as Xenopus, sea urchin and Dictyostelium were different.

Properties and synthesis of ribosomal RNA in the free-living nematode Panagrellus silusiae

The normal S values of ribosomes and ribosomal subunits extracted from the free-living nematode. Panagrellus silusiae are similar to those of other eukaryotic organisms. Upon heating (70 degrees C, 15 min) a 5.5-S RNA is released from the larger ribosomal RNA (27 S; 1.40-10(6) daltons). Unlike other protostomes, however, the 27-S rRNA does not dissociate in an orderly manner to yield 18-S components. The electrophoretic mobility of the small ribosomal RNA species (18 S; 0.72-10(6) daltons) is unaltered by heat treatment. The base composition of both Panagrellus rRNA species has a 51% G+C content. Labelling worms with either [Me-3H] methionine or [14C] uridine at various stages of postembryonic development and subsequent analysis of the extracted RNA revealed eight radioactive fractions, two of which were the mature ribosomal RNAs. From both the time sequence of appearance of the eight RNA species and the relative degree of methylation of the various RNA fractions two maturation pathways for ribosomal RNA processing were deduced. A 37-S (3.6-10(6) daltons) RNA is the precursor to both 27-S and 18-S RNA. During processing about two-fifths of the original transcriptional unit is lost. In this organism the "transcribed spacer" regions may be methylated although alternate interpretations have not been precluded.