The organization of the ribosomal RNA genes of Chironomus tentans and some closely related species

Karyotype and COI gene sequences of Chironomusmelanotus Keyl, 1961 from the Yaroslavl region, Russia, and the difficulties with its identification using GenBank and BOLD systems

Karyotype and COI gene sequences of Chironomusmelanotus Keyl, 1961 from the Yaroslavl region (Russia) were analyzed. A low level of chromosomal polymorphism has been confirmed, eventually eight banding sequences were found: melA1, melB1, melC1, melD1, melE1, melF1, and melG1; only melD2 was found in two larvae from the Sunoga river. Analysis of phylogenetic tree and estimated genetic distances has shown not all COI gene sequences of Ch.melanotus in GenBank and BOLD to belong to this species. The lower distance of 0.4% was observed between two sequences from the Yaroslavl region and Finland, apparently these are true Ch.melanotus sequences. The distances between true Ch.melanotus and other sequences from Finland were 9.5% and 12.4%, and from Sweden it was 11%. The average genetic distance between studied sequences of 9.1% is out of the range of the 3% threshold previously determined for chironomids. According to our estimates, there are two sequences with a distance of 2.9% that may belong to Ch.annularius Meigen, 1818, and one sequence with a genetic distance of 2.1%, may belonging to Ch.cingulatus Meigen, 1830, which has been confirmed karyologically. Another two sequences form a separate cluster. We suggest that they either belong to a known species, but are not present in the databases, or belong to a distinct, undescribed species.

Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers

Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs) located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA), allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.

Ribosomal RNA gene insertions in the R2 site of Rhynchosciara (Diptera: Sciaridae)

Ribosomal RNA genes of most insects are interrupted by R1/R2 retrotransposons. The occurrence of R2 retrotransposons in sciarid genomes was studied by PCR and Southern blot hybridization in three Rhynchosciara species and in Trichosia pubescens. Amplification products with the expected size for non-truncated R2 elements were only obtained in Rhynchosciara americana. The rDNA in this species is located in the proximal end of the X mitotic chromosome but in the salivary gland is associated with all four polytene chromosomes. Approximately 50% of the salivary gland rDNA of most R. americana larval groups analysed had an insertion in the R2 site, while no evidence for the presence of R1 elements was found. In-situ hybridization results showed that rDNA repeat units containing R2 take part in the structure of the extrachromosomal rDNA. Also, rDNA resistance to Bal 31 digestion could be interpreted as evidence for nonlinear rDNA as part of the rDNA in the salivary gland. Insertions in the rDNA of three other sciarid species were not detected by Southern blot and in-situ hybridization, suggesting that rDNA retrotransposons are significantly under-represented in their genomes in comparison with R. americana. R2 elements apparently restricted to R. americana correlate with an increased amount of repetitive DNA in its genome in contrast to other Rhynchosciara species. The results obtained in this work together with previous results suggest that evolutionary changes in the genus Rhynchosciara occurred by differential genomic occupation not only of satellite DNA but possibly also of rDNA retrotransposons.

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.

Chromosome ends in Chironomus pallidivittatus contain different subfamilies of telomere-associated repeats

Tandemly repeated 340 bp sequences, TA repeats, are present in seven of the eight pairs of chromosome ends in Chironomus pallidivittatus, being absent from the telocentric left end of chromosome four. We have previously shown that the family of TA repeats consists of four main subfamilies. One subfamily is composed of a master unit and the other three contain derived units, each of which has a small region where the master sequence is highly mutated. Here we find that there are considerable variations in numbers of TA repeats between animals and for the same telomere in different animals. We also show that the seven telomere pairs containing TA repeats differ with regard to the content of derived subfamilies. The master unit is probably present in all seven pairs. Two of the derived units are exclusively present in two telomere pairs. The third derived unit shows a more irregular distribution. Some of the telomeres have highly variable contents of such units among animals. Subfamilies thus have different behaviour as reflected in their stable and variable patterns of distribution between individual telomeres.

The ribosomal genes of the mosquito, Aedes aegypti

The characterisation of the ribosomal genes of the mosquito, Aedes aegypti, is described. Preliminary experiments using a cloned Drosophila ribosomal DNA (rDNA) repeat to probe Southern transfers of Ae. aegypti genomic DNA has indicated that the rDNA repeat of Ae. aegypti is 9.0 kb in length and that individual rDNA repeats exhibit a high degree of homogeneity with respect to length and the position of restriction enzyme recognition sites within the rDNA. The preliminary mapping data together with partial digestion experiments demonstrate that, as in all other higher eukaryotes, the rDNA repeats are arranged in a head-to-tail, tandemly repeating manner. The restriction mapping of cloned rDNA repeats confirmed the largely uniform length of the Ae. aegypti rDNA repeat and provided a more detailed physical map of the DNA. A restriction site polymorphism was detected in one clone (Aar9) which contains an extra HincII site, which is not present in three other clones studied (Aar1, Aar3, or Aar7). Transcription mapping has allowed the allocation of identities to the various restriction fragments and the approximate positioning of the transcription unit. The estimate of rDNA repeat copy number in Ae. aegypti (approximately 500 copies per haploid genome) is similar to the estimate reported for the closely related species, Aedes albopictus, of 430 copies per haploid genome. Ribosomal DNA thus comprises approximately 0.6% of the total Ae. aegypti genome. Analysis of the variation of the rDNA repeat unit both within individual mosquitoes and between strains of Ae. aegypti, has severed to confirm the remarkable homogeneity of the rDNA repeat unit in this insect.

Allocyclic behaviour and underreplication of the nucleolus chromosome in Pseudodiamesa (Chironomidae)

The chironomid midge Pseudodiamesa branickii shows three polytene, banded elements in salivary gland and Malpighian tubule cells, none of which carry a nucleolar organizer. The present investigation revealed four chromosome pairs in mitotic metaphases, the nucleolus was localized in the tiny chromosome 4. Microphotometric determinations of the DNA contents in mitotic and salivary gland nuclei of Ps. branickii yielded a 2C value of 0.23 pg DNA and a maximum level of 12 endoreplications. In both salivary glands and Malpighian tubules, chromosome 4 appeared as a nonbanded network of chromatin in Feulgen preparations. Indirect immunofluorescent staining with antibodies specific for RNA X DNA hybrids indicated that this structure was transcriptionally active. Its reaction to heavy metal staining suggested that it included the nucleolar organizer, and this was conclusively demonstrated by in situ hybridization with 125I-rRNA. Chromosome pair 4 comprises about 11.4% of the total DNA in metaphase, but only 3.7% in the highly polytene salivary gland complement. According to a numerical simulation, the degree of underrepresentation suggests that about 70% of chromosome 4 is precluded from polytenization. The allocyclic aspect is probably due to this underreplication, with the nucleolar activity causing a structural loosening of the rest of the chromosome. The possible nature of the underreplicated sequences is discussed in the light of recent work on molecular aspects of rDNA structure in various Diptera.

Structural organization of the two main rDNA size classes of Ascaris lumbricoides

The two main rDNA size classes in the genome of Ascaris lumbricoides consist of 8.8 kb and 8.4 kb long repeating units present in a quantitative ratio of roughly 10:1. They both contain the genes coding for 18 , 5.8S and 26S ribosomal RNAs. The length heterogeneity is due to a 450 bp long spacer region localized in the longer repeating unit which begins 870 bp upstream of the 5'-end 18S gene. A few additional microheterogeneities in base sequence occur at the 5'-end of the 26S gene. The 18S, 5.8S and 26S coding regions have been mapped on both the 8.8 kb and 8.4 kb repeating units and the localization of the 5'- and 3'-ends of the 18S and 26S genes has been performed by S1 protection. No intervening sequences are present in either coding region of the two main rDNA size classes.

Selective exposure of antigenic determinants in chromosomal proteins upon gene activation in polytene chromosomes

The immunological accessibility of the nucleosomal core protein H3 and non-histone protein, HMG-1, was studied in transcriptionally active regions of Chironomus thummi polytene chromosomes. Chromosomal loci were decondensed by incubating isolated salivary glands in various salt solutions or hemolymph. Indirect immunofluorescence studies on these chromosomes using anti-sera to histone H3 revealed that the puffed regions were depleted of fluorescence. The lack of fluorescence could be correlated with the degree of puffing and the level of transcriptional activity. The puffed regions fluoresce after anti-H3 addition if the chromosomes are not cross-linked with formaldehyde, and if prior to the addition of antibodies the chromosomes are treated with 45% acetic acid. We conclude that, whereas histone H3 is present in the puffed regions, its antigenic determinants are sterically hindered by components which are extractable by 45% acetic acid. On the other hand, the antigenic determinants of protein HMG-1 are always available to antibody binding in puffed regions, as well as other chromosomal areas.

Spacer size heterogeneity in ribosomal DNA of Chironomus thummi is due to a 120 bp repeat homologous to a predominantly centromeric repeated sequence

The rDNA of Ch. tepperi is homogeneous in structure with a repeat size of 8.4 kb. This size seems to be typical for the basic repeat unit in Chironomus species. Ch. th. piger rDNA cistrons are slightly increased in length (9.0 kb). In the non-transcribed spacer (NTS) an appr. 0.18 kb segment is additionally present in about 50% of the repeats. Ch. th. thumni DNA contains largely heterogeneous rDNA repeats, mainly between 10 and 16 kb. The heterogeneity is due to varying numbers of 120 bp elements present in the NTS. The different spacer size classes are not randomly distributed. The short repetitive 120 bp elements (Cla I elements) hybridize in situ with the nucleolus and with centromere regions. The Cla I elements are regularly present in the thummi NTS, but are absent in the piger NTS. Only very few piger rDNA cistrons may contain Cla I elements.

Cloning and characterization of the ribosomal RNA genes of Rhynchosciara americana

The ribosomal RNA genes (rDNA) of Rhynchosciara americana were analysed using Southern transfers of DNA cleaved with EcoRI, HindIII, BamHI and PstI. The results show that the rDNA is heterogeneous in structure. Following digestion with EcoRI and hybridization to rRNA three bands corresponding to fragments of 9.5, 7.5 and 5.5 kilobases (kb) were detected. Recombinants containing EcoRI fragments of R. americana DNA were prepared using the vector lambda gt lambda B. Three different recombinants (lambda gt Ra1, lambda gt Ra23 and lambda gt Ra5) were isolated containing the rDNA fragments of 9.5, 7.5 and 5.5 kb, respectively. These fragments were transferred to pBR325 and analysed with restriction enzymes and Southern hybridization with 28 S and 18 S rRNA. The lambda gt recombinants were further analysed by R-loop mapping. The data show that the rDNA occurs in two different repeating gene units. A shorter repeat of 9.5 kb and a longer repeat of 13 kb, in which the 28 S rRNA coding sequence contains an insertion of 3.5 kb.

Cloning and analysis of ribosomal DNA of Chironomus thummi piger and Chironomus thummi thummi. The nontranscribed spacer of Ch. th. thummi contains a highly repetitive DNA sequence

The ribosomal DNAs from Ch. thummi piger and Ch. th. thummi were cloned and analysed by a variety of restriction endonucleases. Comparison of rDNA clones from the two subspecies revealed a considerable length difference: the length of the analysed rDNA cistrons is approximately 9.0 kb for Ch. th. piger and approximately 14.5 kb for Ch. th. thummi. The nearly 5 kb additional DNA in Ch. th. thummi is clearly located within the non-transcribed spacer region, and consists of AT-rich, repetitive DNA elements. These elements with a basic repeat length of approximately 120 bp, are arranged tandemly in stretches of up to about 50 identical copies, which are characterized by a cleavage site for ClaI restriction endonuclease. They are found only in the Ch. th. thummi rDNA clones and not in the Ch. th. piger clones. Southern hybridizations between cloned ribosomal DNA and "centromeric" highly repetitive DNA have shown that the ribosomal repetitive Cla-elements are closely related to a highly repetitive DNA sequence family, which is present in various chromosomal sites particularly the centromeres. Sequence analysis has revealed more than 90% homology between the ribosomal Cla-elements and the "centromeric" Cla-elements.--Since it is clear from cytological investigations that Ch. th. piger with the small rDNA repeating unit is the phylogenetically older subspecies, we postulate a transposition of Cla-elements into the nucleolar DNA during the evolution of Ch. th. thummi.

Study of salivary gland specific transcripts in Chironomus tentans by cDNA analysis

Preparative amounts of polyA-containing RNA were purified from isolated salivary glands from Chironomus tentans and used as a template for the synthesis of cDNA by AMV reverse transcriptase. The yield of cDNA corresponded to 8-14% of the input polyA RNA. Using the Alwine hybridization method (Alwine et al., 1977) it was shown that only a minor part of the cDNA hybridized to the 75S RNA band and that the major hybridization occurred to a hitherto unknown gland-specific polyA RNA transcript of 1.3 kb length. In addition, the cDNA hybridized to a gland-specific polyA-RNA transcript of 2 kb length. - The majority of the cDNA had a size of 0.4 or 0.7 kb in equal amounts. A Southern hybridization of the cDNA to an EcoRI digest of genomic DNA showed in addition to a very weak hybridization to the 40 kb band of the Balbiani ring genes, hybridization to several restriction fragments with sizes from 1.3 to 16 kb.

RNA polymerase III from Drosophila hydei pupae. Purification and partial characterization

DNA-dependent RNA polymerase III, which is usually highly resistant to alpha-amanitin, has been purified from Drosophila hydei pupae. The enzyme is insensitive to alpha-amanitin concentrations up to 0.1 microM; at 100 microM alpha-amanitin the enzyme activity is inhibited by approximately 10%. The enzyme was extracted at low ionic strength and purified to homogeneity by six purification steps; 0.1--0.2 mg enzyme/kg pupae could be obtained. The subunit composition of the enzyme was determined after sucrose-gradient centrifugation by sodium dodecyl sulphate electrophoresis in polyacrylamide gels. The enzyme was resolved into putative subunits of molecular weight 154 000, 135 000, 62 000, 58 000, 38 000, 32 000, 31 000, 27 200, 26 500, 21 500 and 17 500. This subunit composition is in general accord with that of eucaryotic class III enzymes. The catalytic properties (salt-activation profile, ratio of activity with denatured DNA to that with native DNA) and the order of elution of the enzyme from DEAE-cellulose with respect to RNA polymerase II agree with the classification of the isolated enzyme as an RAN polymerase III.