Transfer RNA genes of Drosophila melanogaster

A Drosophila melanogaster transfer RNA gene cluster at the cytogenetic locus 90BC

We report the isolation and characterization of a 31 X 10(3) base-pair DNA segment containing a cluster of Drosophila melanogaster transfer RNA genes from the cytogenic locus 90BC. Seven distinct coding regions have been identified in a 15 X 10(3) base-pair DNA segment. These coding regions contain at least ten tRNA structural genes and include sequences encoding the following tRNAs: tRNAval, tRNAPro, tRNAAla and tRNAThr. We have determined the nucleotide sequence of six of these structural genes and their flanking regions. These genes do not contain intervening sequences nor do they encode the terminal CCA. The tRNA genes from the locus also appear to be functional when assayed in a Xenopus germinal vesicle in vitro transcriptional system.

Analysis of chromosomal homologies between two species of the subgenus Sophophora: D. miranda and D. melanogaster using cloned DNA segments

Chromosomal homology between two species of the subgenus Sophophora, D. miranda and D. melanogaster, belonging to the obscura and the melanogaster group respectively, was probed by DNA in situ cross hybridizations. A set of recombinant plasmids with inserts derived from the D. melanogaster genome were cross hybridized to the D. miranda karyotype. Vice versa, recombinant Lambda phages isolated from a genomic D. miranda library were localized in D. miranda and probed for localization in D. melanogaster. In the main, the results support the homology relations proposed on the basis of cytogenetic data. However, the location of both tandemly repetitive genes tested, 5S RNA genes and the histone genes, is not in accordance with expectation. The 5S RNA genes, when probed with the D. melanogaster plasmid 12D8 (Artavanis-Tsakonas et al., 1977), were found to occur at two sites in both, D. miranda and D. pseudoobscura.

Post-transcriptional nucleotide addition is responsible for the formation of the 5' terminus of histidine tRNA

All sequenced histidine tRNAs have one additional nucleotide at the 5' end when compared to other tRNA species. Sequence analysis of histidine tRNA genes from Drosophila melanogaster and Schizosaccharomyces pombe showed that the terminal guanylate residue of the mature tRNAs is not encoded by the genes. Analysis of the products from in vitro transcription of these genes in extracts from Drosophila Kc cells demonstrated that the 5'-terminal nucleotide present in the mature tRNA is added post-transcriptionally. The addition reaction requires ATP. A portion of the mature tRNAs are then modified at the 5'-terminal pG. Analysis of the RNA species formed during the in vitro maturation of the Drosophila histidine tRNA primary transcript uncovered the following maturation scheme: (i) the primary transcript is processed by RNase P at the 5' end to form an intermediate precursor; (ii) the 3'-flanking sequence is endonucleolytically removed, and a guanylate moiety is added to the 5' end to form mature-sized histidine tRNA; and (iii) a fraction of the 5'-terminal guanylate residues then undergoes modification. In contrast to the capping of eukaryotic mRNA, the guanylate addition to histidine tRNA results in the formation of a (3'-5')-phosphodiester bond. There are no precedents for the post-transcriptional addition of nucleotides (in phosphodiester linkage) to the 5' end of RNA precursors.

Localization of tRNA genes of Drosophila melanogaster by in situ hybridization

Six purified tRNAs labeled with 125I by chemical or enzymatic methods were hybridized to polytene chromosomes of Drosophila melanogaster. The main chromosomal regions of hybridization wer: tRNAGly(GGA), 58A, 84C, and 90E; tRNALeu(2), 44E, 66B5-8, and 79F; tRNASer(2b), 86A, 88A9-12, and 94A6-8; tRNAThr(3), 47F and 87B; tRNAThr(4), 93A1-2; and tRNATyr(1 gamma), 19F, 22F-23A, 41, 50C1-4 and 85A. At 50C the hybridization of tRNATyr(1 gamma) was polymorphic in the giant strains. When the hybridization of three valine isoacceptors studied previously was re-investigated, it was found that only one hybridization site, 90BC, was shared between tRNAVal(3b) and tRNAVal(4). tRNAVal(3a) did not have any sites in common with the other two.

Immunological method for mapping genes on Drosophila polytene chromosomes

A method is described for localizing DNA sequences hybridized in situ to Drosophila polytene chromosomes. This procedure utilizes a biotin-labeled analog of TTP that can be incorporated enzymatically into DNA probes by nick-translation. After hybridization in situ, the biotin molecules in the probe serve as antigens which bind affinity-purified rabbit antibiotin antibodies. The site of hybridization is then detected either fluorimetrically, by using fluorescein-labeled goat anti-rabbit IgG, or cytochemically, by using an anti-rabbit IgG antibody conjugated to horseradish peroxidase. When combined with Giemsa staining, the immunoperoxidase detection method provides a permanent record that is suitable for detailed cytogenetic analysis. This immunological approach offers four advantages over conventional autoradiographic procedures for detecting in situ hybrids: (i) the time required to determine the site of hybridization is decreased markedly, (ii) biotin-labeled probes are chemically stable and give reproducible results for many months; (iii) biotin-labeled probes appear to produce less background noise than do radiolabeled probes; and (iv) the resolving power is equal to and often greater than that achieved autoradiographically.

The initiator tRNA genes of Drosophila melanogaster: evidence for a tRNA pseudogene

We have isolated four segments of Drosophila melanogaster DNA that hybridize to homologous initiator tRNAMet. Three of the cloned fragments contain initiator tRNA genes, each of which can be transcribed in vitro. The fourth clone, pPW568, contains an initiator tRNA pseudogene which is not transcribed in vitro by RNA polymerase III. The pseudogene is contained in a 1.15 kb DNA fragment. This fragment has the characteristics of dispersed repetitive DNA and hybridizes in situ to at least 30 sites in the Drosophila genome. The arrangement of the initiator tRNA genes we have isolated, is different to that of other Drosophila tRNA gene families. The initiator tRNA genes are not clustered nor intermingled with other tRNA genes. They occur as single copies within an approximately 415-bp repeat segment, which is separated from other initiator tRNA genes by a mean distance of 17 kb. In situ hybridization to polytene chromosomes localizes these genes to the 61D region of the Drosophila genome. Hybridization analysis of genomic DNA indicates the presence of 8-9 non-allelic initiator tRNA genes in Drosophila melanogaster.

Rapid and high resolution detection of in situ hybridisation to polytene chromosomes using fluorochrome-labeled RNA

Fluorochrome-labeled RNA allows the rapid detection of in situ hybrids without the need for long exposure times as in the autoradiographical hybridisation methods. Resolution is high because of the high resolving power of fluorescence microscopy. The application of a previously reported method for the hybrido-cytochemical detection of DNA sequences to polytene chromosomes of Drosophilia is described. The specificity and sensitivity of the method are demonstrated by the hybridisation with polytene chromosomes of 1) rhodamine-labeled 5S RNA, to the 5S rRNA sites of D. melanogaster (56F) and D. hydei (23B), 2) rhodamine-labeled RNA complementary to a plasmid containing histone genes, to the 39DE region of D. melanogaster, 3) rhodamine-labeled D. melanogaster tRNA species (Gly-3 and Arg-2), to their respective loci in D. melanogaster, 4) rhodamine-labeled RNA complementary to the insert of plasmid 232.1 containing part of a D. melanogaster heat shock gene from locus 87C, to D. hydei heat shock locus 2-32A. In the latter instance it was possible to demonstrate the labeling of a double band which escaped unambiguous detection by autoradiography in the radioactive cytochemical hybridisation procedure because of the low topological resolution of autoradiograms. The sensitivity of the fluorochrome-labeled RNA method is compared with the radioactive methods which use 3H- or 125 I-labeled RNAs. The factors governing the sensitivity and the number of bound fluorochrome molecules to be expected are discussed.

The genes coding for tRNA Tyr of Drosophila melanogaster: localization of determination of the gene numbers

Transfer RNA(Tyr) (anticodon G psi A) was isolated from Drosophila melanogaster by means of Sepharose 4B, RPC-5, and polyacrylamide gel electrophoresis. The rRNA was iodinated in vitro with Na125 I and hybridized in situ to salivary gland chromosomes from Drosophila. The genes of rRNA(Tyr) were localized in eight regions of the genome by autoradiography. Restriction enzyme analysis of genomic DNA indicated that the haploid Drosophila genome codes for about 23 tRNA(Tyr) genes. The regions 22F and 85A each contain four to five tRNA(Tyr) genes, whereas the regions 28C, 41AB, 42A, 42E, and 56D each contain two to three tRNA(Tyr) genes.

Mammalian tRNA genes: nucleotide sequence of rat genes for tRNAAsp, tRNAGly and tRNAGlu

A cloned 2.1 kb fragment of rat DNA hybridized to purified tRNAAsp has been sequenced. The result revealed that in addition to the putative gene for tRNAAspGAU(C), the fragment contained the tRNAGlyGGA(G) and tRNAGluGAG genes. The genes for tRNAAsp, tRNAGly and tRNAGlu have the same polarity, are arranged in this order and are regularly separated by DNA regions of about 450 bp. These rat genes contain neither intervening sequences nor the CCA sequence expected in the 3'-end of the mature tRNA. As observed in lower eukaryotic tRNA genes, the 5'-flanking regions of the three rat genes do not have any significant sequence homology as a regulatory element. In the 3'-flanking region, the sequences CTTTTTG and CTTTTG are present 11 bp downstream from the 3'-end of the genes for tRNAAsp and tRNAGly, respectively. The same CTTTTG sequence is repeated twice in regions 47 and 60 bp away from the tRNAGlu gene. The short T cluster common to the three genes might be the transcription termination site as in lower eukaryotic tRNA genes.

The localization of tRNA5Asn, tRNAHis, and tRNAAla genes from drosophila melanogaster by in situ hybridization to polytene salivary gland chromosomes

Transfer RNA5 gammaAsn, tRNA gamma His, and tRNAAla were isolated from Drosophila melanogaster by means of Sepharose 4B chromatography and 2-dimensional polyacrylamide gel electrophoresis. The tRNAs were iodinated in vitro with Na125I and hybridized in situ salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNA 5 gammaAsn in the regions 42A, 59F, 60C, and 84F; for tRNAHis in the regions 48F and 56E; and for tRNAAla in the regions 63A and 90C. From these and our previous results it can be concluded that the genes for the Q-base containing tRNAs (tRNAAsn, tRNAAsp, and tRNAHis, are not clustered in the Drosophila melanogaster genome.

The nucleotide sequence of histidine tRNA gamma of Drosophila melanogaster

The nucleotide sequence of D. melanogaster histidine tRNA gamma was determined to be: pG-G-C-C-G-U-G-A-U-C-G-U-C-psi-A-G-D-G-G-D-D-A-G-G-A-C-C-C-C-A-C-G-psi-U-G-U-G- m1G-C-C-G-U-G-G-U-A-A-C-C-m5C-A-G-G-U-psi-C-G-m1A-A-U-C-C-U-G-G-U-C-A-C-G-G-m5C -A-C-C-AOH. An additional unpaired G is found at the 5' end, and the T in the TpsiC loop is replaced by a U.