Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci

Sequence analysis of mitochondrial DNA in a mouse cell line resistant to chloramphenicol and oligomycin

A mouse L-cell line, designated 111-OB3, is described which is resistant to two drugs, chloramphenicol and oligomycin. The cells contain two types of mitochondrial DNA molecules, in roughly equal proportions, which differ in that one is cleaved by endonuclease EcoRI at a novel site within the coding sequence for subunit 6 of the mitochondrial ATPase (ATPase-6). Sequence analysis reveals that the cleavage site was created by a single transversion which predicts a replacement of valine in the wild-type ATPase-6 by glutamic acid. The replacement occurs in a hydrophobic amino acid sequence which is highly conserved in mouse, human, and bovine proteins. The position of the replacement is similar to a substitution observed in one class of yeast mutants resistant to oligomycin. Both of the mitochondrial DNA molecules in 111-OB3 also have a single nucleotide change in the gene encoding the large (16S) rRNA. These observations are consistent with the hypothesis that oligomycin resistance in mammalian cells can be cytoplasmically determined and can result from alterations in ATPase-6. The appearance of the mutation before selection in oligomycin suggests a model for the origin of mitochondrial mutations in mammalian cells.

Homologous proteins encoded by yeast mitochondrial introns and by a group of RNA viruses from plants

Hensgens et al. (1983a) have demonstrated the existence of distant homology (averaging 19.6%) between the central sections of seven proteins encoded by introns (and one product of an apparently independent gene) in yeast mitochondrial DNA. The homologous regions are typically segments of about 115 amino acids within open reading frames of about 10(3) bases. Genetic studies indicate that at least two of these proteins are required for the splicing of mitochondrial transcripts. This paper reports that two distantly related proteins of Mr 30,000 that are encoded by different strains of tobacco mosaic virus both contain central sections whose amino acid sequences are 15% to 23% identical in a single alignment to those of one group of four intron-encoded proteins, and possess certain groups of conserved residues also characteristic of the mitochondrial proteins. Genetic studies implicate these proteins in the spreading of viral lesions. While this level of identity cannot establish conclusively that the proteins are related, it suggests the possibility of a functional and/or evolutionary connection that would, if borne out, have important implications.

An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae

We have localized ten oxi3- mutations in the first, al1, intron of the coxl gene. All are splicing deficient, being unable to excise the intron. Complementation experiments disclose several domains in the intron al1: the 5'-proximal and 3'-proximal domains harbor cis-dominant mutations, while trans-recessive ones are located in the intron's open reading frame. Comprehensive analyses of allele-specific polypeptides accumulating in mutants show that they result from the translation of the intron's ORF. We conclude that a specific mRNA maturase involved in splicing of oxidase mRNA is encoded by the intron al1 in a manner similar to the cytochrome b mRNA maturase.

Part of the 23S RNA located in the 11S RNA fragment is a constituent of the ribosomal peptidyltransferase centre

Upon irradiation, 3-[4-benzoylphenyl]propionyl-PhetRNA bound to the P-site of poly(U)-primed ribosomes is exclusively cross-linked to 23S RNA. It is shown that the photoreaction only occurs with pyrimidine nucleotides. The site of the cross-link is located within an 11S RNA fragment, which comprises the 1100 nucleotides at the 3'-end of 23S RNA. The cross-linked Phe tRNA derivative is still functionally active in peptide bond formation. The site labelled on the 11S fragment is therefore an integral part of the peptidyltransferase centre.

The intron of the mitochondrial 21S rRNA gene: distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae

We have screened numerous different yeast species for the presence of sequences homologous to the intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (intron r1) and found them in all Kluyveromyces species, some of the Saccharomyces species and none of the other yeasts tested. We have determined the nucleotide sequence of the r1-intron in K. thermotolerans and compared it with that of S. cerevisiae. The two introns are inserted at the same position within the 21S rRNA gene. They contain homologous internal open reading frames (ORFs) initiated at the same AUG codon which can be aligned over their entire length. Several silent multi-substitutions indicate that these intronic ORFs represent selectively conserved functional genes. Other intron segments, on the contrary, reveal short blocks of extensive homology separated by non-homologous stretches and/or additions-deletions. Comparison of our two yeast r1-introns with equivalent introns of N. crassa and A. nidulans mitochondria reveals that introns with very similar RNA secondary structures can accommodate different types of ORFs.

Sequence analysis of mitochondrial DNA in a mouse cell line resistant to chloramphenicol and oligomycin

A mouse L-cell line, designated 111-OB3, is described which is resistant to two drugs, chloramphenicol and oligomycin. The cells contain two types of mitochondrial DNA molecules, in roughly equal proportions, which differ in that one is cleaved by endonuclease EcoRI at a novel site within the coding sequence for subunit 6 of the mitochondrial ATPase (ATPase-6). Sequence analysis reveals that the cleavage site was created by a single transversion which predicts a replacement of valine in the wild-type ATPase-6 by glutamic acid. The replacement occurs in a hydrophobic amino acid sequence which is highly conserved in mouse, human, and bovine proteins. The position of the replacement is similar to a substitution observed in one class of yeast mutants resistant to oligomycin. Both of the mitochondrial DNA molecules in 111-OB3 also have a single nucleotide change in the gene encoding the large (16S) rRNA. These observations are consistent with the hypothesis that oligomycin resistance in mammalian cells can be cytoplasmically determined and can result from alterations in ATPase-6. The appearance of the mutation before selection in oligomycin suggests a model for the origin of mitochondrial mutations in mammalian cells.

pif mutation blocks recombination between mitochondrial rho+ and rho- genomes having tandemly arrayed repeat units in Saccharomyces cerevisiae

Three allelic nuclear mutants affected in the recombination of mtDNA have been characterized in Saccharomyces cerevisiae and assigned to the PIF locus. In the mutants, the general recombination measured by the recombination frequency between linked or unlinked alleles is normal. However, the pif mutations prevent the integration into the rho+ genome of the markers (oli1, oli2, diu1, ery, oxi1, oxi2) of those rho- genomes that have tandemly arrayed repeat units. Therefore, these rho- genomes characterize a PIF-dependent recombination system. The pif mutations have also revealed the existence of a PIF-independent recombination system used by those rho- genomes that have an inverted organization of their repeat units. The markers of such palindromic rho- genomes exhibit high integration frequency into the rho+ genome even in the presence of the pif mutation. In addition, the pif mutations greatly increase suppressiveness in crosses between pif rho+ strains and PIF-dependent as well as PIF-independent rho- clones. We conclude that the recombination between rho+ and rho- genomes involves at least two distinct systems that depend on the organization of the rho- genome.

Comparison of sea urchin and human mtDNA: evolutionary rearrangement

Clones of full-length mtDNA have been isolated from a Strongylocentrotus franciscanus recombinant DNA library by screening a cDNA clone of cytochrome oxidase subunit 1 mRNA. Restriction fragment cross-hybridization analysis shows the following difference in gene arrangement between sea urchin and human mtDNA. The 16S rRNA and cytochrome oxidase subunit 1 genes are directly adjacent in sea urchin mtDNA. These two genes are separated in human and other mammalian mtDNAs by the region containing unidentified reading frames 1 and 2. In spite of the difference in gene order, gene polarity appears to have been conserved. We conclude that the difference in gene order reflects a rearrangement that took place in the sea urchin lineage since sea urchins and mammals last shared a common ancestor.

Close relationship between certain nuclear and mitochondrial introns. Implications for the mechanism of RNA splicing

We present the first indication of a direct relationship between a nuclear and a mitochondrial splicing system. The intron in the precursor of the large, nuclearly coded ribosomal RNA of two species of Tetrahymena possesses all the features of a class of fungal mitochondrial introns. Sequences conserved in mitochondrial introns of different fungal species are also found in the same order in these Tetrahymena nuclear introns, and the intron RNA can be folded to form a secondary structure similar to that proposed for mitochondrial introns by Davies et al. (1982). This "core" secondary structure brings the ends of the intron together. Furthermore, the first intron in the precursor of the large, nuclearly coded rRNA of Physarum polycephalum also has the characteristic conserved sequences and core RNA secondary structure. The limited sequence data available suggest that the intron in the large rRNA of chloroplasts in Chlamydomonas reinhardtii also resembles the mitochondrial introns. Tetrahymena large nuclear rRNA introns also have an internal sequence that can act as an adaptor by pairing with upstream and downstream exon sequences adjacent to the splice junctions to precisely align the splice junctions. These nuclear introns therefore fit the model of the role of intron RNA in the splicing process that was proposed by Davies et al. (1982), suggesting that the mechanisms of splicing may be very similar in these apparently diverse systems. It is therefore probable that the RNA secondary structures for which there is good evidence in the case of mitochondrial introns will be found to form the basis of active site structure and precise alignment in splicing and cyclization of the Tetrahymena intron "ribozyme".

Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences

Splicing of the ribosomal RNA precursor of Tetrahymena is an autocatalytic reaction, requiring no enzyme or other protein in vitro. The structure of the intervening sequence (IVS) appears to direct the cleavage/ligation reactions involved in pre-rRNA splicing and IVS cyclization. We have probed this structure by treating the linear excised IVS RNA under nondenaturing conditions with various single- and double-strand-specific nucleases and then mapping the cleavage sites by using sequencing gel electrophoresis. A computer program was then used to predict the lowest-free-energy secondary structure consistent with the nuclease cleavage data. The resulting structure is appealing in that the ends of the IVS are in proximity; thus, the IVS can help align the adjacent coding regions (exons) for ligation, and IVS cyclization can occur. The Tetrahymena IVS has several sequences in common with those of fungal mitochondrial mRNA and rRNA IVSs, sequences that by genetic analysis are known to be important cis-acting elements for splicing of the mitochondrial RNAs. In the predicted structure of the Tetrahymena IVS, these sequences interact in a pairwise manner similar to that postulated for the mitochondrial IVSs. These findings suggest a common origin of some nuclear and mitochondrial introns and common elements in the mechanism of their splicing.

Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo

In previous studies of RNA splicing in vitro, we have shown that the intervening sequence (IVS) of the Tetrahymena rRNA precursor is excised as a unique linear RNA molecule and subsequently cyclized. In the present work, we have investigated the occurrence and stability of these RNA species in vivo. RNA was separated by gel electrophoresis, transferred to diazotized paper, and hybridized with 32P-labeled DNA probes. RNA molecules containing the IVS were found to reside within the nucleus and not in the cytoplasm. The species found in nucleus include both the linear and circular forms of the excised IVS RNA, as well as the unspliced precursor. On the basis of quantitation of the hybridization, the half-lives of the IVS-containing pre-rRNA and the excised IVS RNA in rapidly growing cells were estimated as 2 and 6 s, respectively. We conclude that splicing is not a rate-limiting step in rRNA maturation and that the IVS RNA is quickly degraded after its excision. When the deproteinized nuclear RNA was incubated at 37 degrees C in a Mg2+-containing solution, a substantial portion of the linear IVS RNA was converted to the circular form. Autocyclization, previously characterized with IVS RNA produced by splicing in vitro, is therefore also a property of IVS RNA produced in vivo.

Two intron sequences in yeast mitochondrial COX1 gene: homology among URF-containing introns and strain-dependent variation in flanking exons

The DNA sequences of two optional introns in the gene for subunit I of cytochome c oxidase in yeast mitochondrial DNA have been determined. Both contain long unassigned reading frames (URFs). These display regions of amino acid homology with six other URFs, two of which encode proteins involved in mitochondrial RNA splicing. Such conserved regions may thus define functionally important domains of proteins involved in RNA processing. This homology also implies that these URFs had a common ancestral sequence, which has been duplicated and dispersed around the genome. Comparison of the flanking exons in the long strain KL14-4A with their unsplit counterpart in D273-10B reveals clustered sequence differences, which lead in D273-10B to codons rarely used in exons. These differences may be linked to the loss or absence of one of the optional introns.

Characterization of chloramphenicol- and 8-azaguanine-resistant mutants isolated from a continuous rat-liver epithelial cell line

2 non-tumorigenic, chloramphenicol- and 8-azaguanine-resistant strains have been isolated from the rat-liver cell line K-22, by a 2-step mutagenesis procedure. Their chromosome composition and growth properties have been characterized. Failure of chloramphenicol to inhibit mitochondrial protein synthesis in one of the clones, F1, strongly suggests that resistance to the antibiotic in this strain is due to a mutation in mitochondrial DNA.

Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria

The mitochondrial gene coding for the large ribosomal RNA (21S) has been isolated from a rho- clone of Saccharomyces cerevisiae. A DNA segment of about 5500 base pairs has been sequenced which included the totality of the sequence coding for the mature ribosomal RNA and the intron. The mature RNA sequence corresponds to a length of 3273 nucleotides. Despite the very low guanine-cytosine content (20.5%), many stretches of sequence are homologous to the corresponding Escherichia coli 23S ribosomal RNA. The sequence can be folded into a secondary structure according to the general models for prokaryotic and eukaryotic large ribosomal RNAs. Like the E.coli gene, the mitochondrial gene contains the sequences that look like the eukaryotic 5.8S and the chloroplastic 4.5S ribosomal RNAs. The 5' and 3' end regions show a complementarity over fourteen nucleotides.

The major transcripts of the kinetoplast DNA of Trypanosoma brucei are very small ribosomal RNAs

The nucleotide sequence has been determined of a 2.2 kb segment of kinetoplast DNA, which encodes the major mitochondrial transcripts (12S and 9S) of Trypanosoma brucei. The sequence shows that the 12S RNA is a large subunit rRNA, although sufficiently unusual for resistance to chloramphenicol to be predicted. The 9S RNA has little homology with other rRNAs, but a possible secondary structure is not unlike that of the 2.5-fold larger E. coli 16S rRNA. We conclude that the 12S RNA (about 1230 nucleotides) and the 9S RNA (about 640 nucleotides) are the smallest homologues of the E. coli 23S and 16S rRNAs yet observed.

Structural variations and optional introns in the mitochondrial DNAs of Neurospora strains isolated from nature

Mitochondrial DNAs from ten wild-type Neurospora crassa, Neurospora intermedia, and Neurospora sitophila strains collected from different geographical areas were screened for structural variations by restriction enzyme analysis. The different mtDNAs show much greater structural diversity, both within and among species, than had been apparent from previous studies of mtDNA from laboratory N. crassa strains. The mtDNAs range in size from 60 to 73 kb, and both the smallest and largest mtDNAs are found in N. crassa strains. In addition, four strains contain intramitochondrial plasmid DNAs that do not hybridize with the standard mtDNA. All of the mtDNA species have a basically similar organization. A 25-kb region that includes the rRNA genes and most tRNA genes shows very strong conservation of restriction sites in all strains. The 2.3-kb intron found in the large rRNA gene in standard N. crassa mtDNAs is present in all strains examined, including N. intermedia and N. sitophila strains. The size differences between the different mtDNAs are due to insertions or deletions that occur outside of the rRNA-tRNA region. Restriction enzyme and heteroduplex mapping suggest that four of these insertions are optional introns in the gene encoding cytochrome oxidase subunit I. Mitochondrial DNAs from different wild-type strains contain zero, one, three, or four of these introns.

Analysis of a yeast nuclear gene involved in the maturation of mitochondrial pre-messenger RNA of the cytochrome oxidase subunit I

We have analyzed the mitochondrial RNA of a yeast nuclear pet mutant with no cytochrome oxidase activity. The product of the gene affected in this mutant appears to be necessary for the correct maturation of the mitochondrial pre-mRNA of the cytochrome oxidase subunit I. It does not affect, however, the overall splicing of cytochrome b pre-mRNA or the intron excision of the 21S ribosomal RNA precursor. This gene has been isolated by genetic complementation in yeast, and its DNA sequence has been determined. It is transcribed, as detected by S1 mapping experiments, and could encode a protein of 436 amino acids.

Making ends meet: a model for RNA splicing in fungal mitochondria

On the basis of available nucleotide sequence and genetic data; we present a model for RNA splicing in fungal mitochondria. Seven intron RNAs of two fungal species can form identical secondary structures, involving four conserved sequences, which bring the ends of each intron together and allow an internal guide RNA sequence to pair with exon bases adjacent to the splice junctions. The splicing sites are thus aligned precisely within a conserved structure, which we suggest could present specific recognition signals to the proteins that catalyse the splicing reaction.

Genetics of mitochondrial ribosomes of yeast: mitochondrial lethality of a double mutant carrying two mutations of the 21S ribosomal RNA gene

Among the mitochondrial conditional mutations localized in the gene coding for the 21S ribosomal RNA, one--ts 902--produces severely reduced amounts of 21S RNA and 50S subunit. We investigated its physiological properties and found that this thermosensitive mutation was associated with highly pleiotropic effects. The mutant phenotype is associated with cell death in certain conditions, and with a massive accumulation of rho- mutants at non-permissive temperature. Furthermore, interactions with the sites of action of erythromycin and chloramphenicol, both localized within the 21S rRNA, were detected. The mutant is hypersensitive to erythromycin and has a cis-incompatibility with the chloramphenicol-resistant mutation CR321. Ts 902 thus appears to have a dual effect, not only at the ribosomal level but also at a cellular level.

Intron within the large rRNA gene of N. crassa mitochondria: a long open reading frame and a consensus sequence possibly important in splicing

We describe the sequence of the 2295 nucleotide long intron and 245 nucleotides of the flanking exon sequences within the large (24S) rRNA gene of Neurospora crassa mitochondria. The intron contains a long open reading frame, which could correspond to ribosomal protein S5. Comparison with the corresponding intron of the large rRNA gene of yeast mitochondria reveals a single highly homologous 57 nucleotide long sequence, including the sequence (formula; see text), which is present in virtually all the sequenced introns of yeast, Aspergillus nidulans and Zea mays mitochondrial genes, and which may be important for their processing. Sequences closely related to this consensus sequence are also present within all four of the introns of nuclear rRNA genes which have been sequenced. The intron is located within a highly conserved region of the large rRNA sequence and at exactly the same site as in the corresponding introns in yeast mitochondria and also in Physarum polycephalum nuclei.

Drosophila mitochondrial DNA: a novel gene order

Part of the replication origin-containing A+T-rich region of the Drosophila yakuba mtDNA molecule and segments on either side of this region have been sequenced, and the genes within them identified. The data confirm that the small and large rRNA genes lie in tandem adjacent to that side of the A+T-rich region which is replicated first, and establish that a tRNAval gene lies between the two rRNA genes and that URF1 follows the large rRNA gene. The data further establish that the genes for tRNAile, tRNAgln, tRNAf-met and URF2 lie in the order given, on the opposite side of the A+T-rich region to the rRNA genes and, except for tRNAgln, are contained in the opposite strand to the rRNA, tRNAval and URF1 genes. This is in contrast to mammalian mtDNAs where all of these genes are located on the side of the replication origin which is replicated last, within the order tRNAphe, small (12S) rRNA, tRNAval, large (16S) rRNA, tRNAleu, URF1, tRNAile, tRNAgln, tRNAf-met and URF2, and, except tRNAgln, are all contained in the same (H) strand. In D. yakuba URF1 and URF2, the triplet AGA appears to specify an amino acid, which is again different from the situation found in mammalian mtDNAs, where AGA is used only as a rare termination codon.

Identification of two erythromycin resistance mutations in the mitochondrial gene coding for the large ribosomal RNA in yeast

Two independent erythromycin resistance mutations, ER514 and ER221, have been identified in the mitochondrial gene coding for the 21S ribosomal RNA. The two mutations were found to be identical, corresponding to a A to G transition at the nucleotide position 1951 of the ribosomal RNA gene. In the secondary structure model of the ribosomal RNA, the ER resistance site is found at the proximity of the chloramphenicol resistance sites located about 500 bases downstream.

Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure

The complete sequences of nine Saccharomyces cerevisiae mitochondrial introns, six of which carry long open reading frames, have already been published. We have recently determined the sequence of an intron in the large ribosomal mitochondrial RNA of Kluyveromyces thermotolerans (Jacquier et al., in preparation), which we found to be closely related to its S. cerevisiae counterpart. This latter result prompted us to undertake a systematic search for possible homologous elements in the other, available sequences with the help of an original computer program. A previously unsuspected wealth of evolutionarily conserved sequences and secondary structures was thus uncovered. Seven at least of the available sequences may be folded up into elaborate secondary structure models, the cores of which are nearly identical. These models result in bringing together the exon-intron junctions into relatively close spatial proximity and looping out either all or most of the sequences in open reading frame, when present. These results and their possible implications with respect to the mechanism of splicing are discussed in the light of available genetic and biochemical data.

Internal structure of a mitochondrial intron of Aspergillus nidulans

The intron of the mitochondrial apocytochrome b gene, cobA, of Aspergillus nidulans has been subjected to sequence analysis. It contains an open reading frame of 957 base pairs contiguous with the preceding exon. Regions of the translated open reading frames of cobA and the third intron of the cob gene in yeast show high amino acid homology. Comparison of the cobA intron with this and other yeast introns indicates that cobA codes for a maturase protein that splices out the intron encoding it and possibly other mitochondrial introns. Two very similar decamer peptides are found in the protein sequences of the cobA intron, four mitochondrial yeast introns, and the yeast mitochondrial sequence reading frame 1 (RF-1) and may be diagnostic of one class of maturase-coding introns. Four short DNA sequences, two of which are in the region defined by box9 and box2 mutations in the cob gene of yeast, are conserved in cobA and certain yeast introns. Comparison with three yeast introns strongly suggests that the first 200 base pairs of the open reading frame of the cobA intron do not code for any amino acids present in the putative maturase protein but are required for splicing or the control of splicing, or both.

Erythromycin resistance due to a mutation in a ribosomal RNA operon of Escherichia coli

There are seven ribosomal RNA operons (rrn operons) in Escherichia coli. A single rrn operon was amplified by use of a multicopy recombinant plasmid containing a complete rrnH operon. rrnH thereby has the potential to contribute a greater fraction of the rRNA found in ribosomes. Erythromycin-resistant mutants were isolated from cells containing the plasmid, and at least one mutation to resistance was shown to reside in rrnH on the plasmid. Erythromycin resistance was retained when a major deletion was introduced into the 16S rRNA gene and was abolished by deletions that affect the 16S and 23S rRNA genes but do not alter the 5S rRNA gene or non-rrnH DNA. Cell-free S30 protein-synthesizing extracts from cells containing the mutant plasmid have an increased resistance to erythromycin. The selection procedure used to isolate erythromycin-resistance mutations in rrnH may allow, with minor modifications, the isolation of mutations in rrn operons that change resistance of the ribosome to other antibiotics or that alter other properties of ribosomes.

Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins, four tRNAs and L-rRNA

The complete nucleotide sequence of a 14 kb segment of A. nidulans mtDNA reveals a rather compact organization of genes transcribed from the same strand and coding for two functionally known proteins, seven unidentified polypeptides (URFs), 24 tRNAs and two rRNAs. One of the URFs is located in the intron of the L-rRNA gene and codes for a basic protein of 410 residues. The other URFs are in spacer regions and code for hydrophobic proteins. URFa is homologous to human URF4, and URFb produces a polypeptide of 48 residues resembling the human URF6L product (hydrophobic N-terminus, basic C-terminus). The ATPase subunit 6 genes from mitochondria and E. coli appear to share a common ancestor. The codon frequencies of identified genes and URFs are similar, and codons ending with G or C are rarely used. The structures of tRNAs specific for arginine, asparagine, tyrosine and histidine are deduced from gene sequences.

Mitochondrial L-rRNA from Aspergillus nidulans: potential secondary structure and evolution

The alignment of gene sequences coding for A. nidulans mitochondrial L-rRNA and E. coli 23S rRNA indicates a strong conservation of primary and potential secondary structure of both rRNA molecules, except that homologies to the 5'-terminal 5.8S-like region and the 3'-terminal 4.5S-like region of bacterial rRNA are not detectable on mtDNA. The structural organization of the A. nidulans mt L-rRNA gene corresponds to that of yeast omega + strains: both genes are interrupted by a large intron sequence (1678 and 1143 bp, respectively) and by another smaller insert (91 and 66 bp) at homologous positions within domain V. An evolutionary tree derived from conserved L-rRNA gene sequences of yeast nuclei, E. coli, maize chloroplasts and six mitochondrial species exhibits a common root of organelle and bacterial sequences separating early from the nuclear branch.

The anticodon of the maize chloroplast gene for tRNA Leu UAA is split by a large intron

The maize chloroplast gene encoding tRNA Leu UAA has been sequenced. It contains a 458 base pair intron between the first and second bases of the anticodon. The tRNA is 88 nucleotides long (the 3'-terminal CCA sequence included which, however, is not encoded by the gene) and differs in only four nucleotides (modified nucleotides are not considered) from the corresponding isoacceptor from bean chloroplasts. The unusual position of the intron in this maize chloroplast tRNA gene suggests a splicing model different from that generally accepted for eukaryotic split tRNA genes.

A design for computer nucleic-acid-sequence storage, retrieval, and manipulation

We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base ("the library") and software that manages and provides access to that data base ("the Librarian").

The complete nucleotide sequence of a 23-S rRNA gene from tobacco chloroplasts

The nucleotide sequence of a tobacco chloroplast 23-S rRNA gene, including the spacer between it and the 4.5-S rRNA gene, has been determined. The 23-S rRNA coding region is 2804-base-pairs long. A comparison with the 23-S rRNA sequence of Escherichia coli reveals strong homology and further shows a similarity between the chloroplast 4.5-S rRNA and the 3'-terminal region of E. coli 23-S rRNA. However, the 101-base-pair spacer sequence between the 23-S and 4.5-S rRNA genes has little homology with E. coli 23-S rRNA.