Base sequence complexity of the stable RNA species of Drosophila melanogaster

Structural analysis of a bovine arginine tRNA(CCG) gene

A bovine genomic clone containing a 17.4-kb DNA fragment was isolated and found to contain a solitary arginine tRNA gene with an anticodon of CCG that has a 100% identity to its cognate tRNA. This arginine tRNA gene, symbolized as TRR4, has a characteristic internal split promoter and a typical termination site for RNA polymerase III. The tRNA gene was transcribed in vitro by RNA polymerase III using a HeLa cell-free extract to yield a mature-sized tRNA product. The gene was mapped to bovine chromosome 19 using a panel of bovine-rodent somatic cell hybrid DNAs.

Conservatism of sites of tRNA loci among the linkage groups of several Drosophila species

The sites of seven tRNA genes (Arg-2, Lys-2, Ser-2b, Ser-7, Thr-3, Thr-4, Val-3b) were studied by in situ hybridization. 125I-labeled tRNA probes from Drosophila melanogaster were hybridized to spreads of polytene chromosomes prepared from four Drosophila species representing different evolutionary lineages (D. melanogaster, Drosophila hydei, Drosophila pseudoobscura, and Drosophila virilis). Most tRNA loci occurred on homologous chromosomal elements of all four species. In some cases the number of hybridization sites within an element varied and sites on nonhomologous elements were found. It was observed that both tRNA(2Arg) and tRNA(2Lys) hybridized to the same site on homologous elements in several species. These data suggest a limited amount of exchange among different linkage groups during the evolution of Drosophila species.

Extensive microheterogeneity of serine tRNA genes from Drosophila melanogaster

The nucleotide sequences of nine genes corresponding to tRNA(Ser)4 or tRNA(Ser)7 of Drosophila melanogaster were determined. Eight of the genes compose the major tRNA(Ser)4,7 cluster at 12DE on the X chromosome, while the other is from 23E on the left arm of chromosome 2. Among the eight X-linked genes, five different, interrelated, classes of sequence were found. Four of the eight genes correspond to tRNA(Ser)4 and tRNA(Ser)7 (which are 96% homologous), two appear to result from single crossovers between tRNA(Ser)4 and tRNA(Ser)7 genes, one is an apparent double crossover product, and the last differs from a tRNA(Ser)4 gene by a single C to T transition at position 50. The single autosomal gene corresponds to tRNA(Ser)7. Comparison of a pair of genes corresponding to tRNA(Ser)4 from D. melanogaster and Drosophila simulans showed that, while gene flanking sequences may diverge considerably by accumulation of point changes, gene sequences are maintained intact. Our data indicate that recombination occurs between non-allelic tRNA(Ser) genes, and suggest that at least some recombinational events may be intergenic conversions.

Nucleotide sequence and transcription of a human tRNA gene cluster with four genes

A bacteriophage lambda clone containing a 20-kb human DNA segment was isolated and found to harbor a cluster of four tRNA genes. An 8.2-kb HindIII subfragment encompassing the genes was cloned into pBR322 for restriction mapping and DNA sequence analysis. The genes were found to be arranged as two tandem pairs, separated by 3 kb. A proline tRNAAGG gene is separated from a leucine tRNAAAG gene by a 724-bp intergenic region in the first pair, and a second proline tRNAAGG gene is 316 bp from a threonine tRNAUGU gene in the second pair, with the leucine tRNA gene being of opposite polarity to the other three genes. A putative Alu-like element was found to occur within a 2.0-kb DNA fragment, at least 0.7 kb from the tRNA gene cluster. The coding sequences of the two proline tRNAAGG genes are identical. The coding regions of all four tRNA genes contain consensus internal split promoter sequences and do not have intervening sequences nor the CCA trinucleotide found in mature tRNAs. The 3'-flanking regions of these four tRNA genes have normal RNA polymerase III termination sites of at least four consecutive T nucleotides. No apparent homologies occur between the 5'-flanking regions of these genes. All four tRNA genes are accurately transcribed in an in vitro HeLa cell-free system, and the RNase T1 fingerprints of the mature-sized tRNA transcripts were found to be consistent with the DNA sequences of the genes.

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.

Genes and pseudogenes in a reiterated rat tRNA gene cluster

A 13.4 kb rat genomic DNA fragment containing two related tRNA gene clusters was isolated from a rat lambda recombinant and analyzed for gene arrangement and nucleotide sequence. One cluster was found to contain a tRNALeuCUG gene while the second contained a tRNALeuCUA pseudogene with multiple base substitutions. The tRNALeu gene was found to possess an intact coding region and a functional transcription termination signal at the 3' end as demonstrated by in vitro transcription and processing of precursors to mature size tRNA. The first tRNA gene cluster was found to contain in addition to tRNALeu, three other transcribable genes coding for tRNAAspGAC(U), tRNAGlyGGA(G) and tRNAGluGAG; the second cluster contained in addition to tRNALeu pseudogene, the tRNAAsp tRNAGly and tRNAGlu genes. Examination of flanking sequences of the corresponding tRNA genes in the two clusters shows no homology at the 5' ends and partial conservation of sequences at the 3'-end region. Genomic rat DNA blot hybridizations show that the tRNALeu gene is distributed together with the tRNAAsp, tRNAGly and tRNAGlu on a 10 fold repeat of 3.2 kb EcoRI fragment.

Nucleotide sequences of two regions of the human genome containing tRNAAsn genes

The primary structures of two human tRNAAsn genes and 600-700 nucleotides of their flanking regions have been determined from two separate isolates of a fetal DNA library in phage lambda vector. The tRNA gene from one clone differs from the major mammalian tRNAAsn by a single base substitution at position 47, with an A replacing a G, while the tRNAAsn gene from the second clone has base substitutions at positions 17 and 65, with a G replacing a C and a T replacing a C, respectively. The sequences of the noncoding 5'- and 3'-flanking regions of both clones are over 90% homologous. As with other mammalian tRNA genes, these two human tRNAAsn genes contain CTTTTPu, which might act as a transcription termination signal, 11 bp 3' to the structural gene. In vitro transcription experiments in a HeLa cell extract demonstrate that both cloned tRNAAsn genes can be transcribed and processed to mature-sized tRNAs.

Molecular cloning, sequence analysis and in vitro expression of a rat tRNA gene cluster

A rat genomic DNA fragment containing a tRNA gene cluster was isolated from a lambda phage library. Hybridization and nucleotide sequence analysis revealed the presence of a 83 bp tRNALeuCUG gene and a 72 bp tRNAAspGUG gene. Both genes possessed intact coding regions and putative transcription termination signals at their respective 3' ends. In vitro transcription analysis of the two subcloned genes in a HeLa cell S-100 system demonstrated the specific synthesis of a number of RNAs by RNA polymerase III. Studies carried out in the presence of alpha-amanitin showed that the larger RNAs are precursors for the final processed transcripts of the tRNALeu and tRNAAsp genes, respectively. Further nucleotide sequence analysis of the cluster revealed the presence of tRNAGly and a tRNAGlu pseudogenes with missing areas within their coding regions which are essential for transcription by RNA polymerase III. Within the region of DNA between the tRNALeu and tRNAAsp genes is a sequence which is 65% homologous to a region of the rat B1 element. The significance of this latter structure within the gene cluster is unknown.

A rat tRNA gene cluster containing the genes for tRNAPro and tRNALys. Analysis of nucleotide sequences of the genes and the surrounding regions

A lambda clone carrying a rat DNA fragment of 11.9 kb was isolated from a rat gene library with total rat tRNA as a probe. Nucleotide sequence analysis revealed that the DNA fragment contained six tRNA genes, three for tRNAPro and three for tRNALys. Of the six genes all but one tRNAPro gene have the same polarity. Each tRNA gene is separated by a DNA region of 0.1 to 3.6 kb. The 5'-flanking regions of the six rat genes in the cluster do not have any significant sequence homology, but in the 3'-flanking region, each gene has a short T cluster, which is supposed to be a transcription termination signal.

Genes for tRNALys5 from Drosophila melanogaster

The sequences of two cloned genes from Drosophila which hybridize with tRNALys5 are reported. One gene, in plasmid pDt39, has a sequence which corresponds to the sequence of tRNA. The other gene, in pDt59R, differs in three nucleotides pairs. Both plasmids are transcribed in vitro with extracts of Drosophila Kc cells to give full-sized tRNA precursors with four additional nucleotides at the 5'-end as well as truncated molecules containing 35 nucleotides. This premature termination occurs in a block of four T residues within the mature coding region. Sequences flanking the tRNA genes show little in common except for the blocks of five or more T-residues beyond the 3'-end of the gene. pDt39 hybridizes to 84AB on the polytene chromosomes of Drosophila and pDt59R hybridizes to 29A.

Characterization of a rat tRNA gene cluster containing the genes for tRNAAsp, tRNAGly and tRNAGlu, and pseudogenes

The putative genes for tRNAGAUAsp(C), tRNAGGAGly(G) and tRNAGAGGlu are in a cluster on the rat chromosome and are present exclusively in a 3.3 kb region cleaved with a restriction endonuclease EcoRI. The cluster reiterates about 10 times on the haploid DNA. Four lambda clones each containing an independent repeating unit were isolated from a rat gene library. The studies on the cloned DNA revealed that the length of the repeating unit including the 3.3 kb EcoRI fragment was at least 13.5 kb. Nucleotide sequence analysis of the 3.3 kb DNA in the isolated clones showed sequence variations among the repeating units and incomplete genes for tRNAGly and tRNAGlu within the clusters.

Isolation and characterization of cloned rat DNA fragment carrying tRNA genes

A rat genomic library was screened for tRNA genes with an unfractionated rat liver tRNA probe. About 70 clones containing tRNA genes were detected per rat genome. The organization of tRNA genes in five clones was analyzed by restriction endonuclease digestion, RNA-DNA hybridization and in vitro transcription with nuclear extracts from Xenopus oocytes. Evidence is presented suggesting that tRNA genes are distributed in the rat genome in small clusters spanning 1 to 2 kb and interspersed with large regions (minimum 8 to 20 kb) of non tRNA-coding DNA. The tRNA gene clusters were found to contain the sequences for a variety of tRNA species. Genes for a single isoacceptor, were found in more than one clone. The detailed study of one clone shows the repetition of a cluster of four tRNA sequences at a distance of about 8 kb. The arrangement of tRNA genes in rat appears to follow the irregular pattern of tRNA gene organization previously reported in Drosophila and Xenopus.

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.

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 structure and function of tRNA genes of higher eukaryotes

The most recent findings concerning the structure and function of tRNA genes of higher eukaryotes are discussed in an exemplary way. The tRNA genes of higher organisms are either dispersed or clustered at different sites of the genome. Clusters contain tRNA genes oriented in both directions and on both strands of the DNA with spacers of various length inbetween. Some genes contain intervening sequences close to the 3' side of the anticodon. The primary transcription product possesses a 5' leader and a 3' trailer sequence which are removed by several maturation steps in a strict temporal and spacial order. Internal transcription control regions (promotors) are located at the 5' and 3' ends of the mature tRNA coding section of the tRNA gene. External sequences modulating the efficiency of the expression are present at the immediate 5' ends of the genes. Transfer RNA genes are located nonrandomly in the nucleosomes.

Analysis of a drosophila tRNA gene cluster: two tRNALeu genes contain intervening sequences

A recombinant DNA phage containing a cluster of Drosophila melanogaster tRNA genes has been isolated and analyzed. The insert of this phage has been mapped by in situ hybridization to chromosomal region 50AB, a known tRNA site. Nucleotide sequencing of the entire Drosophila tRNA coding region reveals seven tRNA genes spanning 2.5 kb of chromosomal DNA. This cluster is separated from other tRNA regions on the chromosome by at least 2.7 kb on one side, and 9.6 kb on the other. Two tRNA genes are nearly identical and contain intervening sequences of length 38 and 45 bases, respectively, in the anticodon loop. These two genes are assigned to be tRNALeu genes because of significant sequence homology with yeast tRNA3Leu, and secondary structure homology with yeast tRNA3Leu intervening sequence. In addition, an 8 base sequence (AAAAUCUU) is conserved in the same location in the intervening sequences of Drosophila tRNALeu genes and a yeast tRNA3Leu gene. Similar sequenes occur in all other tRNAs containing intervening sequences. The remaining five genes are identical tRNAIle genes, which are also identical to a tRNAIle gene from chromosomal region 42A. The 5' flanking regions are only weakly homologous, but each set of isoacceptors contains short regions of strong homology approximately 20 nucleotides preceding the tRNA coding sequences: GCNTTTTG preceding tRNAIle genes; and GANTTTGG preceding tRNALeu genes. The genes are irregularly distributed on both DNA strands; spacing regions are divergent in sequence and length.

Two drosophila melanogaster tRNAGly genes are contained in a direct duplication at chromosomal locus 56F

One Drosophila melanogaster tRNAGly gene occurs on each 1.1-2.0 kb unit of a direct duplication at chromosomal region 56F. The nucleotide sequence of the gene and the 5' flanking region has been determined. The non-transcribed strand sequence of the tRNA gene is: 5' GCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCA 3'. This nucleotide sequence is identical to that of the major glycine tRNA in Bombyx mori posterior silk gland. Within the 22 kb region mapped, additional tRNA genes are found, an observation consistent with reports that genes for other isoacceptors are present at this locus.

The gross anatomy of a tRNA gene cluster at region 42A of the D. melanogaster chromosome

The sequence organization and positions of the tRNA genes in a tRNA gene cluster at chromosomal region 42A of the D. melanogaster (Dm) genome have been studied by recombinant DNA methods. A set of overlapping inserts of Dm DNA cloned in a lambdoid vector and extending in both directions from the Drosophila tRNA gene-bearing fragment of plasmid pCIT12 has been isolated by the procedure of "chromosomal walking." The isolated region has a total length of 94 kb of which a central 46 kb region contains eight tRNAAsn genes, four tRNA2Arg genes, five tRNA2Lys genes and one tRNAIle gene. The genes are irregularly spaced and transcribed from both strands; they occur to some extent in subclusters. Thus this sequence organization is totally different from the tandem repeat organizaiton seen in many 5S rRNA gene clusters of higher eucaryotes and in one Xenopus rRNA gene clusters of higher eucaryotes and in one Xenopus tRNA gene cluster.

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.

Evolution of a D. melanogaster glutamate tRNA gene cluster

We have determined the DNA sequence of a cloned cluster of essentially identical glutamate tRNA genes of D. melanogaster. The cluster consists of five genes: a gene triplet spanning approximately 0.55 kb followed by a 0.45 kb gene doublet 3.0 kb downstream. The genes are all arranged with the same polarity, do not encode the tRNA CCA end and contain no intervening sequences. Examination of the 5' and 3' sequences immediately flanking each gene reveals a striking pattern of sequence homologies between certain of the genes, which suggests a possible evolutionary history of this gene cluster. We propose that two ancestral genes each gave rise to gene doublets by duplication, while one of these gene pairs then gave rise, in turn, to a trio of genes as a result of unequal crossover.

Transfer RNA genes of Drosophila melanogaster

Three recombinant plasmids containing randomly sheared genomic D. melanogaster tRNAs have been identified and characterized in detail. One of these, the plasmid 14C4, has a D. melanogaster (Dm) DNA segment of 18 kb, and has three tRNA2Arg and two tRNAAsN genes. The second plasmid, 38B10, has tRNAHis genes, while the third plasmid, 63H5, contains coding sequences for tRNA2Asp. The Dm DNA segments in each recombinant plasmid are derived from unique cytogenetic loci. 14C4 is from 84 F, 38B10 is from 48 F and 63H5 is from 70 A.

Hybridization of tRNAs of Drosophila melanogaster to polytene chromosomes

Highly purified tRNAs from Drosophila melanogaster were iodinated with 125I and hybridized to squashes of polytene chromosomes of Drosophila silivary glands followed by autoradiography to localize binding sites. Most tRNAs hybridize strongly to more than one site and weakly to one or more additional sites. The major sites for various tRNAs are the following: tRNA2Arg, 42A, 84F1,2; tRNA2Asp, 29DE; tRNA3Gly, 22BC, 35BC, 57BC, tRNA2Lys, 42A, 42E; tRNA5Lys, 84AB, 87B; tRNA2Met, 48B5-7, 72F1-2, 83F-84A; tRNA3Met, 46A1-2, 61D1-2, 70F1-2; tRNA4Ser, 12DE, 23E; tRNA7Ser, 12DE, 23E; tRNA3aVal, 64D; tRNA3bVal, 84d3-4, 92b1-9; tRNA4Val, 56D3-7, 70BC.

A cloned Drosophila DNA fragment which codes for a 4 S RNA species

A collection of random Drosophila melanogaster DNA fragments cloned individually in Escherichia coli was screened for the presence of sequences complementary to the 4 S, 5 S and 5.8 S RNA species produced in the D. melanogaster Kc tissue culture line. Four D. melanogaster DNA fragments were found which possessed sequences complementary to the 4 S RNA species but not complementary to the 5 S or 5.8 S RNA. One such cloned fragment (6.81 kilobase in length) was characterized further. It hybridizes in situ to region 22A-C of the left arm of chromosome 2 and does not contain repetitive sequences detectable by renaturation (cot) analysis. This same region was reported earlier by Steffensen and Wimber (Genetics (1971) 69, 163--178) to hybridize in situ to bulk tRNA extracted from D. melanogaster.

Sequence arrangement of tRNA genes on a fragment of Drosophila melanogaster DNA cloned in E. coli

A plasmid with the vector Col E1 attached to an insert of Drosophila melanogaster DNA carrying four tRNA genes has been cloned in E. coli. Some features of the sequence arrangement and the positions of the tRNA genes have been determined by electron microscopic methods and by restriction endonuclease mapping. tRNA genes were mapped at 1.4, 4.7, 5.9 and 8.6 kb from one of the Drosophila/Col E1 junctions in the Drosophila insert of total length 9.34 kb. There are several secondary structure features consisting of inverted repeat sequences of length about 70-100 nucleotide pairs, some with and some without intervening loops, irregularly distributed on the insert. Cross-hybridization of tRNAs isolated by hybridization to separated restriction fragments indicate that the tRNA genes at 4.7, 5.9 and 8.6 kb are identical and differ from the one at 1.4 kb. Thus the positions of the genes, of the secondary structure features and of the restriction endonuclease sites all indicate that the spacers between the genes are not identical tandem repeats. In situ hybridization with cRNA transcribed from the plasmid showed localization at region 42A of chromosome 2R.