Glutamate tRNA genes are adjacent to 5S RNA genes in Drosophila and reveal a conserved upstream sequence (the ACT-TA box)

Two complex regions, including a TATA sequence, are required for transcription by RNA polymerase I in Neurospora crassa

In order to define the RNA polymerase I transcriptional apparatus and how it might interact with regulatory signals, the DNA sequences necessary for 40S rRNA transcription in Neurospora crassa were determined. A systematic set of deletion, substitution and insertion mutations were assayed in a homologous in vitro system. The sequences required for transcription of the gene consist of two large domains (I and II) from -113 to -37, and -29 to +4, respectively. Complete deletion of either domain abolished transcription. Upstream sequences confer a small stimulation of transcription. Domain II includes a TATA sequence at -5 which is sensitive to a small (2 bp) substitution and which is conserved among the large rRNA genes of many organisms. Domain I includes a sequence, termed the 'Ribo box', which is also required for transcription of the Neurospora 5S rRNA genes (1), and which occurs in the 5' region of a Neurospora ribosomal protein gene. The 5S and 40S Ribo boxes are shown to be functionally interchangeable.

Sequence analysis of the glutamate tRNA family: evidence for pseudogenes

Human tRNA(CUCGlu) has been isolated by direct hybridization of the tRNA to 28S ribosomal RNA. We now report the isolation of mouse tRNA(CUCGlu) using the same procedure. Partial sequence analysis of the mouse tRNA shows that it is identical to the human tRNA and to a cloned rat tDNA(CUCGlu) sequence. This mouse tRNA(CUCGlu), however, differs by one nucleotide from a previously cloned mouse tDNA(CUCGlu) sequence, suggesting that the tDNA may be a pseudogene. Further evolutionary comparison of these and other glutamate tRNAs and tDNAs has provided evidence to suggest that two other tDNA(Glu) sequences arose by mutation of functional tRNAGlu genes such that their anticodon sequences were converted from one glutamate isoacceptor to the other. These tDNA sequences may also represent pseudogenes.

An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes

The DNA sequences upstream of the 5S RNA genes in Neurospora crassa are largely different from one another, but share a short consensus sequence located in the segment 29 to 26 nucleotides preceding the transcribed region. Differences among flanking sequences do not appear to affect transcription. Deletion analysis indicates, however, that a DNA segment including the conserved "TATA box" is required for in vitro transcription of Neurospora 5S RNA genes.

Concerted evolution of dispersed Neurospora crassa 5S RNA genes: pattern of sequence conservation between allelic and nonallelic genes

About 100 genes coding for 5S RNA in Neurospora crassa are dispersed throughout the genome (Selker et al., Cell 24:815-818, 1981; R. L. Metzenberg, J. N. Stevens, E. U. Selker, and E. Morzycka-Wroblewska, manuscript in preparation). The majority of them correspond to the most abundant species (alpha) of 5S RNA found in the cell. Gene conversion, gene transposition, or both may be responsible for the maintenance of sequence homogeneity (concerted evolution) of alpha-type 5S genes. To explore these possibilities, we isolated and characterized separate 5S regions from two distantly related laboratory strains of N. crassa. Restriction and sequence analyses revealed no differences in molecular location of allelic 5S genes between the two strains. However, the DNA sequences around the 5S genes are ca. 10% divergent. We concluded that transposition is not frequent enough to account for the concerted evolution of N. crassa alpha-5S genes. In contrast to sequence divergence in the flanking regions between the two strains, the 5S transcribed regions are identical (with one exception), suggesting that these genes are being corrected. We have found that flanking sequences of various N. crassa 5S genes within each strain are largely different. Thus, if the correction mechanism is based on gene conversion, it is limited to the transcribed regions of the genes. However, we did find a short region of consensus including the sequence TATA located 25 to 30 nucleotides preceding the position of transcription initiation. This region may be involved in the transcription of N. crassa 5S genes.

Transcription of a Drosophila tRNAArg gene in yeast extract: 5'-flanking sequence dependence for transcription in a heterologous system

The Drosophila tRNA gene encoded on pArg is efficiently transcribed in extracts of Saccharomyces cerevisiae, but the efficiency is 5'-flanking sequence dependent: deletion to between positions -21 and -17 (relative to position +1 of the mature coding sequence) reduces transcription to a very low level. This demonstrates that requirement for wild-type 5'-flanking sequence exists in the case of a heterologous combination of a tRNA gene and transcription extract. Expression of pArg in vivo in S. cerevisiae is also dependent on the wild-type 5'-flanking sequence, but only with deletion to between -17 and -11 is the steady-state level of pArg transcripts reduced to near zero. The 5'-flanking sequence requirement in S. cerevisiae extract is similar to that found in Drosophila Kc cell extract. However, transcription kinetics distinguish S. cerevisiae extract from that of Drosophila Kc cells. tRNA genes added to S. cerevisiae extract exhibit a lag phase before initiation of active transcription, but this lag is much shorter and much less temperature dependent than is the lag phase in Drosophila Kc cell extract.

Concerted evolution of dispersed Neurospora crassa 5S RNA genes: pattern of sequence conservation between allelic and nonallelic genes

About 100 genes coding for 5S RNA in Neurospora crassa are dispersed throughout the genome (Selker et al., Cell 24:815-818, 1981; R. L. Metzenberg, J. N. Stevens, E. U. Selker, and E. Morzycka-Wroblewska, manuscript in preparation). The majority of them correspond to the most abundant species (alpha) of 5S RNA found in the cell. Gene conversion, gene transposition, or both may be responsible for the maintenance of sequence homogeneity (concerted evolution) of alpha-type 5S genes. To explore these possibilities, we isolated and characterized separate 5S regions from two distantly related laboratory strains of N. crassa. Restriction and sequence analyses revealed no differences in molecular location of allelic 5S genes between the two strains. However, the DNA sequences around the 5S genes are ca. 10% divergent. We concluded that transposition is not frequent enough to account for the concerted evolution of N. crassa alpha-5S genes. In contrast to sequence divergence in the flanking regions between the two strains, the 5S transcribed regions are identical (with one exception), suggesting that these genes are being corrected. We have found that flanking sequences of various N. crassa 5S genes within each strain are largely different. Thus, if the correction mechanism is based on gene conversion, it is limited to the transcribed regions of the genes. However, we did find a short region of consensus including the sequence TATA located 25 to 30 nucleotides preceding the position of transcription initiation. This region may be involved in the transcription of N. crassa 5S 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.

Internal promoter elements of transfer RNA genes are preferentially exposed in chromatin

We have examined the chromatin organization of a cluster of transfer RNA genes at the cytogenic locus 90BC on the right arm of the third Drosophila melanogaster chromosome. We find that the internal promoter sequences are preferentially exposed to micrococcal nuclease and DNase I in chromatin. Moreover, these exposed sequences have an unusual single strand nuclease-sensitive conformation.

Transcriptionally active and inactive gene repeats within the D. melanogaster 5S RNA gene cluster

Transcription of isolated repeat units of D. melanogaster 5S DNA in a Drosophila KcO cell extract revealed three types of template activities. 5SI DNA encodes the known 5S rRNA of D. melanogaster and has a relatively high transcription efficiency. 5SII DNA is identical to 5SI DNA except for a two-nucleotide deletion at 5S rRNA positions 28 and 29; the efficiency of transcription is approximately 40% that of 5SI DNA and because of the deletion, the primary transcript is two nucleotides shorter. 5SIII DNA does not support in vitro transcription (less than 2% 5SI DNA), but has the same sequence as 5SI DNA except for a single G to A transition at position 86. This is the first reported point-mutation in a 5S RNA gene resulting in loss of transcription function. Of approximately 23 5S rRNA gene copies in a cloned 5S DNA sub-cluster (p12D1) 19 appear to be of the transcriptionally inactive 5SIII DNA type.

Nucleotide sequence of a yeast tRNAArg3A gene and its transcription in a homologous in vitro system

Twelve bacterial clones containing complementary sequences to yeast tRNAArg3 were isolated from a gene library. The size of the yeast BamHI inserts ranges from 5.4 to 10 MDa. There are at least 6 copies of this gene in different loci of the yeast genome. Insert from clone pYAT-3 was mapped, and the presence of a tRNAArg3A gene was confirmed by DNA sequence. The coding region is colinear with the transcriptional product. Unlike other reported tRNAArg3A genes, this one is not linked to a tRNAAsp gene. In vitro transcription using a yeast extract produces a transcript of 76 +/- 1 bases.

The 5S ribosomal genes in the Drosophila melanogaster species subgroup. Nucleotide sequence of a 5S unit from Drosophila simulans and Drosophila teissieri

The 5S genes of the eight species of the D. melanogaster subgroup have been mapped. The spacers, in contrast with coding regions, differ markedly between most species. One 5S gene unit has been sequenced for both D. simulans and D. teissieri. The mature 5S RNA region in these two species is identical to the corresponding region of D. melanogaster. Only 5 nucleotide variations occur between the D. melanogaster and D. simulans 5S gene spacers. The spacer in D. teissieri is very different. Only two segments, located one at each side of the coding region, are clearly homologous to corresponding sequences of D. melanogaster and D. simulans.

Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp

We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al., 1981, Nucleic Acids Res. 9, 2239-2250). The mouse and rat tRNAAsp and tRNAGly coding regions are identical. The tRNAGlu coding regions differ at two positions. The flanking sequences contain 3 non-homologous areas: a c. 100 bp insertion in the first mouse spacer, short tandemly repeated sequences in the second spacers and unrelated sequences at the 3' ends of the clusters. In contrast, most of the flanking regions are homologous, consisting of strings of consecutive, identical residues (5-17 bp) separated by single base differences and short insertions/deletions. The latter are often associated with short repeats. The homology of the flanking regions is c. 75%, similar to other murine genes. The second lambda clone contains a solitary mouse tRNAAsp gene. The coding region is identical to that of the clustered tRNAAsp gene. The 5' flanking regions of the two genes contain homologous areas (10-25 bp) separated by unrelated sequences. Overall, the flanking regions of the two mouse tRNAAsp genes are less homologous than those of the mouse and rat clusters.

Characterization and nucleotide sequence of a chicken gene encoding an opal suppressor tRNA and its flanking DNA segments

A naturally occurring opal suppressor serine tRNA has been purified from chicken liver and used as a probe to isolate the corresponding gene from a library of chicken DNA in bacteriophage lambda. This minor tRNA is encoded by a single-copy gene that is not part of a tRNA gene cluster. DNA sequence analysis of the gene and its flanking DNA segments shows that the gene is encoded in an 87-base-pair segment without intervening sequences and specifies a tRNA that reads the termination codon UGA. This gene has additional nucleotides in the 5' internal promoter region but has a normal 3' internal promoter sequence and the usual termination signal.

A human tRNAGlu gene of high transcriptional activity

A mixture of low molecular weight RNAs, in which only tRNAs were radiolabelled, was used as a hybridisation probe to select for tRNA-like sequences within a bank of human genomic DNA in lambda Charon 4A. A restriction enzyme digest of one of the selected lambda Charon 4A recombinants contained two fragments (2.4 Kb & 1.8 Kb) which hybridised tRNA and which, when subcloned into pAT153, were transcribed in Xenopus oocyte nuclei. Analysis of the subcloned 2.4 Kb fragment, which was of remarkably high transcriptional activity, revealed the presence of a single gene for tRNAGlu in the middle of the fragment. The sequence immediately preceding the gene has the potential for forming a tRNA-like structure.

Using iodinated single-stranded M13 probes to facilitate rapid DNA sequence analysis--nucleotide sequence of a mouse lysine tRNA gene

From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. However, the mouse gene contains a 14 bp region comprising 13 A-T base pairs, 30-44 bp from the 5' end of the coding region. Cognate A-T rich regions are present in human and Drosophila genes. The coding region is flanked by two 11 bp direct repeats, similar to those associated with alu family sequences. The sequence was determined by a "walking" protocol that employs, as a novel feature, iodinated single-stranded M13 probes to identify M13 subclones which contain sequences partially overlapping and contiguous to an initially determined sequence. The probes can also be used to screen lambda phage and in Southern and dot blot experiments.

Intimate association of 5S RNA and tRNA genes in Drosophila melanogaster

In this communication, we report the isolation of seven new recombinants derived from the 5S gene locus of Drosophila melanogaster. These recombinants can be divided into three different classes. There are four clones derived from within the 5S gene cluster, two which contain non-5S sequences representing the 5'flanking segment of the gene array and have a structure similar to 12D8 described by Artavanis-Tsakonas et al. (1977), and finally one (22A8) which is shown to contain a DNA segment that is located adjacent to the 3' end of the 5S gene cluster. Analysis of these recombinants supports the model in which all 5S genes of our D. melanogaster Oregon-R wild type strain are arranged in one uninterrupted cluster and are transcribed in the same direction. Interestingly, the 2.5 kb of non-5S RNA coding sequences on the recombinant derived from the 3' edge of the cluster contains at least four genes coding for tRNAs and one of these is located less than 300 bp downstream from the last 5S transcription unit. These tRNA genes are shown to be functional on the basis of the ability of 22A8 DNA to direct the synthesis of tRNA in an in vitro transcription system.