A mitochondrial reading frame which may code for a second form of ATPase subunit 9 in Aspergillus nidulans

The nucleotide sequence of a 74 codon reading frame from the Aspergillus nidulans mitochondrial genome is presented. The derived amino acid sequence displays typical features of dicyclohexylcarbodiimide (DCCD) binding proteins and is 84% homologous with a mitochondrial reading frame that potentially encodes an ATPase subunit 9 polypeptide in Neurospora crassa. However, in A. nidulans, as in N. crassa, there is strong biochemical and genetic evidence that this subunit is in fact nuclearly-encoded. In both organisms the DCCD-binding protein found in the F0 complexes of mitochondria from actively-growing cultures is almost certainly the product of this nuclear gene, and definitely not that of the mitochondrial reading frame. The discovery of an intact open reading frame than can code for a DCCD-binding protein in the mitochondrial genome of a second species of filamentous fungus strenghthens the possibility that the presence of a mitochondrial version of this gene has some biological significance.

A comprehensive characterization of a group IB intron and its encoded maturase reveals that protein-assisted splicing requires an almost intact intron RNA

The group I intron (AnCOB) of the mitochondrial apocytochrome b gene from Aspergillus nidulans encodes a bi-functional maturase protein that is also a DNA endonuclease. Although the AnCOB intron self-splices, the encoded maturase protein greatly facilitates splicing, in part, by stabilizing RNA tertiary structure. To determine their role in self-splicing and in protein-assisted splicing, several peripheral RNA sub-domains in the 313 nucleotide intron were deleted (P2, P9, P9.1) or truncated (P5ab, P6a). The sequence in two helices (P2 and P9) was also inverted. Except for P9, the deleted regions are not highly conserved among group I introns and are often dispensable for catalytic activity. Nevertheless, despite the very tight binding of AnCOB RNA to the maturase and the high activity of the bimolecular complex (the rate of 5' splice-site cleavage was >20 min(-1) with guanosine as the cofactor), the intron was surprisingly sensitive to these modifications. Several mutations inactivated splicing completely and virtually all impaired splicing to varying degrees. Mutants containing comparatively small deletions in various regions of the intron significantly decreased binding affinity (generally >10(4)-fold), indicating that none of the domains that remained constitutes the primary recognition site of the maturase. The data argue that tight binding requires tertiary interactions that can be maintained by only a relatively intact intron RNA, and that the binding mechanism of the maturase differs from those of two other well-characterized group I intron splicing factors, CYT-18 and Cpb2. A model is proposed in which the protein promotes widespread cooperative folding of an RNA lacking extensive initial tertiary structure.

The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing

The AnCOB group I intron from Aspergillus nidulans self-splices, providing the Mg2+ concentration is >/= 15 mM. The splicing reaction is greatly stimulated by a maturase protein encoded within the intron itself. An initial structural and biochemical analysis of the splicing reaction has now been performed. The maturase bound rapidly to the precursor RNA (kon approximately 3 x 10(9) M(-1) min(-1)) and remained tightly bound (koff </= 0.04 min(-1)). The catalytic step of 5' splice-site cleavage occurred at a rate of up to 11 min(-1) under single turnover conditions. The maturase-assisted reaction of heat-denatured RNA proceeded at a rate of about 1 min(-1), arguing that there are early steps of folding that cannot be readily facilitated by the protein. pH analysis revealed a biphasic profile with a pKa of 7.0. The rate of the maturase-assisted reaction was independent of the Mg2+ concentration down to 3 mM. Self-splicing in optimal Mg2+ (>/= 150 mM) was tenfold slower, in part because of the existence of an equilibrium between folded and partially folded RNA. In contrast, the maturase very effectively stabilized tertiary structure in 5 mM Mg2+, a noticeable example being an interaction between the P8 helix and a GNRA sequence that constitutes the L2 terminal loop of the P2 helix. Formation of the 5' splice-site recognition helix was assisted by either the maturase or high concentrations of Mg2+. The maturase was required during splicing so it is not a true chaperone. However, RNase protection assays and kinetic studies suggest that the maturase recognizes and facilitates folding of an intron with limited tertiary structure and even incomplete secondary structure.

Self-splicing activity of the mitochondrial group-I introns from Aspergillus nidulans and related introns from other species

The mitochondrial genome of Aspergillus nidulans contains several group-I introns. Each one has been assayed for its ability to self-splice in vitro in the absence of proteins. The intron from the apocytochrome b gene is unusual among subgroup IB4 introns in being able to self-splice, unlike a similar intron from Saccharomyces cerevisiae. The first intron in the cytochrome oxidase subunit-1 gene self-splices but only correctly completes the first step of splicing; cryptic 3' splice-sites are recognized instead and these are also used at a low frequency in vivo. The highly homologous intron from Podospora anserina completes both steps in vitro. The remaining introns do not self-splice. The correlation between subgroup category, the likely presence of specific tertiary interactions, and self-splicing activity is discussed.

A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease

Some group I introns self-splice in vitro, but almost all are thought to be assisted by proteins in vivo. Mutational analysis has shown that the splicing of certain group I introns depends upon a maturase protein encoded by the intron itself. However the effect of a protein on splicing can be indirect. We now provide evidence that a mitochondrial intron-encoded protein from Aspergillus nidulans directly facilitates splicing in vitro. This demonstrates that a maturase is an RNA splicing protein. The protein-assisted reaction is as fast as that of any other known group I intron. Interestingly the protein is also a DNA endonuclease, an activity required for intron mobilization. Mobile elements frequently encode proteins that promote their propagation. Intron-encoded proteins that also assist RNA splicing would facilitate both the transposition and horizontal transmission of introns.

Two group I introns with a C.G basepair at the 5' splice-site instead of the very highly conserved U.G basepair: is selection post-translational?

In virtually all of the 200 group I introns sequenced thus far, the specificity of 5' splice-site cleavage is determined by a basepair between a uracil base at the end of the 5' exon and a guanine in an intron guide sequence which pairs with the nucleotides flanking the splice-site. It has been reported that two introns in the cytochrome oxidase subunit I gene of Aspergillus nidulans and Podospora anserina are exceptions to this rule and have a C.G basepair in this position. We have confirmed the initial reports and shown for one of them that RNA editing does not convert the C to a U. Both introns autocatalytically cleave the 5' splice-site. Mutation of the C to U in one intron reduces the requirement for Mg2+ and leads to an increase in the rate of cleavage. As the C base encodes a highly conserved amino acid, we propose that it is selected post-translationally at the level of protein function, despite its inferior splicing activity.

Deletion of P9 and stem-loop structures downstream from the catalytic core affects both 5' and 3' splicing activities in a group-I intron

The P9 stem-loop is one of the conserved structural elements found in all group-I introns. Using two deletion mutants in this region of the Tetrahymena thermophilia large ribosomal subunit intron, we show that removal of the P9 element, either alone, or together with the non-conserved downstream P9.1 and P9.2 elements, results in an intron incapable of the first step of the splicing reaction at a low concentration of Mg2+. The mutant introns also require high concentrations of Mg2+ for the second step in splicing, as well as hydrolysis reactions, suggesting that P9, as well as P9.1 and P9.2, are important structural elements in the final folded form of the intron. In addition, RNase-T1-mediated-structure-probing experiments demonstrated that the loss of P9, P9.1 and P9.2 changes the structural context of the region binding the 5' splice site. The deletions lead to less efficient recognition of the 3' splice site and an accumulation of unligated exons. These observations support the view that the P9, P9.1 and P9.2 stem-loops play an important role in the binding of the 3' splice site.

The conserved terminal guanosine of a group I intron can help prevent reopening of the ligated exons

The highly conserved terminal guanosine of the Tetrahymena group I intron was mutated to an adenosine. The intron still excised itself but more slowly than the wild-type. At very low concentrations of GTP only ligated exons were produced, but at high concentrations of GTP unligated exons accumulated and the 3' exon acquired a GTP at its 5' end. A series of experiments suggested that GTP was primarily reopening the ligated exons, rather than directly cleaving the 3' splice site. 5' Truncated forms of the wild-type intron can cleave RNA in trans. Cleavage takes place downstream of sequences similar to the last few bases of the 5' exon. The ligated exons would therefore be a potential substrate. We believe that the intron uses the terminal guanosine to compete with exogenous GTP until the ligated exons have dissociated from their binding site. Other interactions between intron sequences which are known to aid in 3' splice-site recognition may assist in this process.

Important 2'-hydroxyl groups within the core of a group I intron

The catalytic activity of a group I intron is dependent on a core structure, much of which is not exposed to solvent. In order to study the structure of the core, an efficient bimolecular reaction has been developed: the 5'-component is a molecule of about 300 bases which contains the 5'-splice-site and terminates in the loop established by P8, and the 3'-component is a 24 base long oligoribonucleotide which includes the 3'-regions of the P8 and P7 helices with their joining region, J8/7. J8/7 is thought to play several roles including binding the helix containing the 5'-splice-site. P7 forms a major portion of the guanosine binding site required for splicing. We have modified the bimolecular system to make it amenable to kinetic analysis and have used it to study the role of the ribose sugars in the oligomer. Multiple deoxyribonucleotide substitution in the J8/7 region completely blocked 5'-splice-site cleavage even though the Kd was only reduced about 5-fold. This supports the idea that the ribose phosphate backbone in J8/7 plays a key role in catalysis. Individual substitutions at G303 and A306 reduced the rate of catalysis 5-10-fold. The G303 substitution blocked GTP-independent hydrolysis of the 5'-splice-site. The region spanning the junction of P8 and J8/7 was also highly sensitive to multiple deoxyribonucleotide substitution; however, only in the case of C298 did an individual substitution have any effect on cleavage. Deoxyribonucleotide substitution in the 3'-section of P7 was less severe, although kcat/Km in low GTP was down 70-fold.

A phosphorothioate at the 3' splice-site inhibits the second splicing step in a group I intron

RNA polymerases can synthesize RNA containing phosphorothioate linkages in which a sulfur replaces one of the nonbridging oxygens. Only the Rp isomer is generated during transcription. A Rp phosphorothioate at the 5' splice-site of the Tetrahymena group I intron does not inhibit splicing (McSwiggen, J.A. and Cech, T.R. (1989) Science 244, 679). Transcription of mutants in which the first base of the 3' exon, U+1, was mutated to C or G, in the presence, respectively, of either cytosine or guanosine thiotriphosphate, introduced a phosphorothioate at the 3' splice-site. In both cases exon ligation was blocked. In the phosphorothioate substituted U+1G mutant, a new 3' splice-site was selected one base downstream of the correct site; despite the fact that the correct site was selected with very high fidelity in unsubstituted RNA. In contrast, the exon ligation reaction was successfully performed in reverse using unsubstituted intron RNA and ligated exons containing an Rp phosphorothioate at the exon junction site. Chirality was reversed during transesterification as in 5' splice-site cleavage (vide supra). This suggests that one non-bridging oxygen is particularly crucial for both splicing reactions.

Primary structure of V-ATPase subunit B from Manduca sexta midgut

The amino acid sequence of a vacuolar-type ATPase (V-ATPase) subunit B has been deduced from a cDNA clone isolated from a Manduca sexta larval midgut library. The library was screened by hybridization with a labeled cDNA encoding subunit B of Arabidopsis thaliana tonoplast V-ATPase. The M. sexta V-ATPase subunit B consists of 494 amino acids with a calculated M(r) of 54,902. The amino acid sequence deduced for V-ATPase subunit B of M. sexta is between 98% and 76% identical with that of seven other V-ATPase subunits B and greater than 52% identical with three archaebacterial ATPase subunits B.

Base pairing between the 3' exon and an internal guide sequence increases 3' splice site specificity in the Tetrahymena self-splicing rRNA intron

It has been proposed that recognition of the 3' splice site in many group I introns involves base pairing between the start of the 3' exon and a region of the intron known as the internal guide sequence (R. W. Davies, R. B. Waring, J. Ray, T. A. Brown, and C. Scazzocchio, Nature [London] 300:719-724, 1982). We have examined this hypothesis, using the self-splicing rRNA intron from Tetrahymena thermophila. Mutations in the 3' exon that weaken this proposed pairing increased use of a downstream cryptic 3' splice site. Compensatory mutations in the guide sequence that restore this pairing resulted in even stronger selection of the normal 3' splice site. These changes in 3' splice site usage were more pronounced in the background of a mutation (414A) which resulted in an adenine instead of a guanine being the last base of the intron. These results show that the proposed pairing (P10) plays an important role in ensuring that cryptic 3' splice sites are selected against. Surprisingly, the 414A mutation alone did not result in activation of the cryptic 3' splice site.

Increasing tubC beta-tubulin synthesis by placing it under the control of a benA beta-tubulin upstream sequence causes a reduction in benA beta-tubulin level but has no effect on microtubule function

We have constructed a chimeric beta-tubulin gene that places the structural gene for the tubC beta-tubulin of Aspergillus nidulans under the control of the benA beta-tubulin promoter. Introduction of either this chimeric gene or a second wild-type benA gene into a benomyl-resistant benA22 strain causes it to become benomyl sensitive, indicating that the introduced genes are functional. Analysis of the tubulin proteins synthesized in benA22 strains into which a second wild-type benA beta-tubulin gene was transformed showed that the total amount of beta-tubulin protein was the same as in the parental strain with a single benA gene. Thus the level of beta-tubulin must be regulated. This was also true of transformants carrying an extra copy of the chimeric beta-tubulin gene. The total amount of beta-tubulin was the same as in the parental strain. Two-dimensional gel analysis showed that the endogenous benA22 and the introduced chimeric tubC gene contributed equally to the total beta-tubulin pool. The fact that one-half of the benA beta-tubulin could be replaced by tubC beta-tubulin with no effect on the growth of the cells suggests that the benA and tubC beta-tubulins are functionally interchangeable.

Identification of phosphate groups important to self-splicing of the Tetrahymena rRNA intron as determined by phosphorothioate substitution

The group I intron from the rRNA precursor of Tetrahymena undergoes self-splicing. The intron RNA catalyst contains about 400 phosphate groups. Their role in catalysis has been investigated using phosphorothioate substituted RNA. In such RNA one of the peripheral oxygens of the phosphodiesters is replaced with sulfur. Incorporation of adenosine 5' phosphorothioate in either the 5' or 3' half of the ribozyme blocked splicing whereas incorporation of uridine 5' phosphorothioate only blocked splicing if the substitution was in the 3' half of the molecule. Modification-interference assays located two major and three minor inhibitory phosphorothioate substitutions suggesting that the corresponding phosphates play a significant role in self-splicing. These are all located in the most highly conserved region of the intron.

Processing of mitochondrial RNA in Aspergillus nidulans

Genes for cytochrome oxidase subunit I (oxiA), ATPase subunit 9, NADH dehydrogenase subunit 3 (ndhC) and cytochrome oxidase subunit II (oxiB) are located within a 7.2 kb (1 kb = 10(3) bases or base-pairs) segment of the Aspergillus nidulans mitochondrial genome. Northern hybridization shows that abundant RNA molecules of 4.0, 2.5 and 1.5 kb, each containing copies of two or more genes, are transcribed from this region. The 4.0 kb molecule, which contains copies of each of the four genes but lacks the three oxiA introns, is cleaved at a point just upstream from ndhC to give rise to the 2.5 kb RNA, which contains copies of oxiA and the ATPase subunit 9 gene, and the 1.5 kb RNA, which carries ndhC and oxiB. The ATPase subunit 9 gene, which has no identified function, is therefore transcribed into an abundant RNA. S1 nuclease analysis indicates that there are no additional introns in the amino-terminal region of oxiA and that the 4.0 and 2.5 kb transcripts of this gene have staggered 5' termini, the most upstream of which is adjacent to the 3' end of the histidinyl-tRNA gene. The results suggest that transcription of this genome proceeds via a very limited number of primary transcripts with mature RNAs produced by extensive processing events including tRNA excision. RNA synthesis and processing in A. nidulans mitochondria therefore resembles the events occurring in metazoa rather than yeast.

Characterization of an inducible expression system in Aspergillus nidulans using alcA and tubulin-coding genes

Plasmids have been constructed in which expression of a gene can be placed under the control of the inducible promoter of the alcA gene encoding alcohol dehydrogenase I in Aspergillus nidulans. Simplified shuttle vectors carrying pyr4 which complements pyrG89 mutations have also been constructed. These are based on pUC19 and retain alpha-peptide expression. The beta-tubulin genes, tubC and benA, have been placed under the control of alcA and their expression studied. Levels of expression can be assayed phenotypically because increased synthesis of beta-tubulin inhibits vegetative growth. Sensitivity of asexual spore formation to the anti-microtubule drug benomyl provides a means of detecting very low levels of expression of the chimeric genes. Glucose almost completely represses the chimeric genes. Induction is rapid and is maximal within an hour. When a strain carrying seven copies of an alcA::tubC gene fusion was grown under inducing conditions, 6.5% of total sulfate labelled protein consisted of tubC product. Cyclopentanone was the most potent inducer of the chimeric genes on solid media but it also partially inhibited growth. Chimeric alcA::tubC and alcA::benA genes were expressed to very similar levels despite the fact that tubC utilizes many rare codons.

The mitochondrial ribosomal RNA molecules of Aspergillus nidulans

The 16S and 23S mitochondrial rRNAs of Aspergillus nidulans have been identified by Northern hybridisation and the ends of the molecules mapped onto the mitochondrial genome by S1 nuclease analysis. The results show that both the rRNA molecules are longer than originally reported, forcing a reassessment of the potential secondary structures that can form in the terminal regions. In particular, structures resembling the 5.8S- and 4.5S-like domains of the bacterial large rRNA can now be recognised within the A. nidulans 23S molecule. The new 5' termini of the 16S and 23S genes lie within conserved 18-bp sequences that may be promoters but are more likely to be processing signals that cleave the mature rRNAs from larger precursor molecules. The new end of the 23S gene abuts the 5' end of the threonine-tRNA gene.

A 'hot-spot' for Ty transposition on the left arm of yeast chromosome III

The small ring derivative of Saccharomyces cerevisiae chromosome III, which was formed by a cross-over between HML on the left arm and HMR on the right arm, contains three Ty elements. The class II element Ty 1-17 lies immediately centromere-distal to LEU2 on the left arm while two class I elements are tandemly arranged distal to PGK on the right arm. We have sequenced the regions of chromosome III surrounding Ty 1-17 and have defined a region where a number of transposition events have occurred. This region is flanked by the 5' ends of two tRNA genes, tRNA3Glu on the centromere distal side and tRNA3Leu immediately in front of LEU2. Close to the tRNA3Glu gene there is a region containing degenerate delta sequences organised in opposite orientations. Immediately distal to Ty 1-17 there are two complete solo delta elements, one inserted into the other. The sequence indicates that these two delta sequences were inserted into chromosome II by separate transposition events. A model is presented to explain how this structure arose and the role of solo delta elements in transposon propagation and maintenance is discussed.

Nucleotide sequence characterization of Ty 1-17, a class II transposon from yeast

We have determined the nucleotide sequence of a class II yeast transposon (Ty 1-17) which is found just centromere-distal to the LEU2 structural gene on chromosome III of Saccharomyces cerevisiae. The complete element is 5961 bp long and is bounded by two identical, directly repeated, delta sequences of 332 bp each. The sequence organization indicates that Ty 1-17 is a retrotransposon, like the class I elements characterized previously. It contains two long open reading-frames, TyA (439 amino acids) and TyB (1349 amino acids). In this paper, the sequences of the two classes of yeast transposon are compared with one another and with analogous elements, such as retroviral proviruses, cauliflower mosaic virus and copia sequences. Features of the Ty 1-17 sequence which may be important to its mechanism of transposition and its genetic action are discussed.

A modified two primer approach to oligonucleotide-directed in vitro mutagenesis

Using oligonucleotide-directed mutagenesis, we are trying to define the features of the protein structure that are important for the DNA and c-AMP binding by CAP from E. coli, the enzymic activity and putative DNA binding of dihydrofolate reductase of L. casei, and the functionally important regions of the self-splicing RNA of the r-RNA intron of Tetrahymena thermophila. We have used a modification of the method described by Norris et al. [1]. A mutagenic primer and an M13 universal sequencing primer are annealed simultaneously to a template from an M13 clone containing the DNA to be mutagenised and, after DNA strand extension, the fragment is cut out and recloned into either M13 or plasmid vectors. We have analysed the effect on the frequency of mutation of: the temperature used for strand extension; the class of base change attempted; the host mismatch repair system. A recently developed system for phenotypic detection of mutations in the Tetrahymena intron aided in determining mutation frequencies.

The Tetrahymena rRNA intron self-splices in E. coli: in vivo evidence for the importance of key base-paired regions of RNA for RNA enzyme function

We have developed an in vivo RNA splicing assay for the self-splicing rRNA intron of Tetrahymena thermophila using E. coli as the host. A DNA fragment containing the intron sequence has been cloned into M13mp83 so that expression of the beta-galactosidase alpha-fragment is dependent upon intron excision from the mRNA precursor. Plaque phenotypes correlate well with levels of excised intron RNA. Point mutations were made by oligonucleotide-directed mutagenesis in conserved sequences P, Q, and S. All showed reduced splicing, agreeing with mitochondrial genetic data for S and providing the first direct evidence that P and Q are functionally important. The results support the hypothesis that base-pairing of R with S and P with Q is important for intron structure and function.

The Aspergillus nidulans mitochondrial genome

A brief description is provided of the overall organisation of the Aspergillus nidulans mitochondrial genome, as revealed by DNA sequence analysis.

Three variant introns of the same general class in the mitochondrial gene for cytochrome oxidase subunit 1 in Aspergillus nidulans

The oxiA gene of Aspergillus nidulans, coding for cytochrome oxidase subunit 1, is shown by DNA sequencing to contain three introns. An AUG start codon is not present at the beginning of the sequence, suggesting that either another codon, possibly the four base codon AUGA, is used for initiation or there is a further short intron between the true start codon and the beginning of the recognisable coding region. The second and third introns have long open reading frames, which could code for maturase proteins. The lack of conservation of amino acid sequence in the putative region of proteolytic cleavage for maturase formation suggests that the first conserved decapeptide may act as the recognition signal for protein processing. The third intron is remarkably (70%) homologous to the second intron of the cytochrome oxidase subunit 1 gene of Schizosaccharomyces pombe and both are located in exactly the same position. The third Aspergillus intron has an in-frame insertion of a 37-bp GC-rich DNA sequence which is now flanked by a 5-bp repeat, a well-known feature of transposable elements. All three introns in the oxiA gene have a 'core' RNA secondary structure found in a class of introns fitting the RNA splicing model of Davies et al. (1982). This core RNA structure may play a catalytic as well as a structural role in intron splicing. A sequence within the intron could act as a guide to align the splice sites of two of the introns in accordance with the model of Davies et al.

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.

Pinching group stabilization. The synthesis and thermal isomerization of 10-Oxapentacyclo[6.3.2.13,6.01,8.02,7]tetradeca-4,12-diene

Sensitized irradiation (benzophenone, 0�, N2, pyrex filter, medium pressure Hg lamp) of dimethyl tricyclo[4.2.1.02,5]nona-3,7-diene-3,4-dicarboxylate (11) in (E)-1,2-dichloroethene yielded a mixture of 1 : 1 adducts (13) and (14) by site selective [2 π+2 π] cycloaddition at the cyclobutene π-bond. Reduction of the (Z)-dichloro isomer(13) with lithium aluminium hydride formed the related diol (16) which is the immediate precursor to the cyclic ether (18). Dechlorination of (18) with zinc in ethanol forms the title diene (19). Thermolysis of the polycyclic diester (20) affords the fragmentation products cyclopentadiene and dimethyl benzene-1,4-dicarboxylate. In contrast, the title compound (19) containing the cyclic ether ring was more stable and yielded the novel isomer (28) as the major product only upon flash vacuum pyrolysis at 560�(1.5 × 10-2 Torr). This difference in behaviour is attributed to a pinching group effect exerted by the cyclic ether present in (19).

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".

DNA duplication has resulted in transfer of an amino-terminal peptide between two mitochondrial proteins

The mitochondrial genome of the ascomycete Aspergillus nidulans possesses at least nine unidentified reading frames (URFs). Two of these are particularly interesting in that the amino acid sequences of the derived translation products are very similar in the N-terminal regions. The first 36 residues of the URFx gene product are repeated at the start of a second reading frame, URFA3, with only six mismatches. Despite this similarity in their amino-termini, the latter parts of URFx and URFA3 are completely different. Closer examination of the nucleotide sequences at the 5' ends of the two genes shows that the conserved peptides are part of a 300-base pair (bp) duplication within the mitochondrial genome. This duplication also includes the tRNA gene for asparagine and a conserved 116-bp intergenic region.

The mitochondnal genome of Aspergillus nidulans contains reading frames homologous to the human URFs 1 and 4

A 2830-bp segment of the mitochondrial genome of the fungus Aspergillus nidulans was sequenced and shown to contain two unidentified reading frames (URFs). These reading frames are 352 and 488 codons in length, and would specify unmodified proteins of mol. wts. 39,000 and 54,000, respectively. The derived amino acid sequences indicate that these genes are equivalent to the human mitochondrial URFs 1 and 4, with 39% amino acid homology for URF1 and 26% for URF4. Both URFs were shown by secondary structure predictions to code for predominantly beta-sheeted proteins with strong structural conservation between the fungal and human homologues. Counterparts of mammalian URFs have not previously been identified in non-mammalian genomes, and the discovery that A. nidulans possesses reading frames so closely homologous with URF1 and URF4 shows that these genes are of general functional importance in the mitochondria of diverse species.

MITOCHONDRIAL FOUR-POINT CROSSES IN ASPERGILLUS NIDULANS: MAPPING OF A SUPPRESSOR OF A MITOCHONDRIALLY INHERITED COLD-SENSITIVE MUTATION

Four-point mitochondrial crosses were conducted in heterokaryons of Aspergillus nidulans. The mutations used were (oliA1), conferring resistance to oligomycin, (camA112), conferring resistance to chloramphenicol; (cs-67), conferring cold-sensitivity, and (sumD16), a suppressor of (cs-67). Initially, the crosses were conducted by observing the segregation of extranuclear markers in heterokaryotic sectors emerging from the original point of heterokaryosis. This showed that (camA112), (cs-67) and (sumD16) were linked but were probably all unlinked to (oliA1). Second, four-point crosses were conducted using a double marker selection technique, in which (camA112) and (oliA1) were always set in repulsion and the frequency of the phenotypes produced by the segregation of the mutant and wild-type alleles of (cs-67) and (sumD) were observed in (camA112 oliA1) recombinants. From these results we concluded that (camA112), (cs-67) and (sumD16) were linked and probably mapped in the order given. It was observed that the two nuclear types of conidia from a heterokaryon often had a dissimilar frequency distribution of the segregants of a mitochondrial cross.

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.

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.

Nucleotide sequence of a region of the mitochondrial genome of Aspergillus nidulans including the gene for ATPase subunit 6

A 1500 bp fragment of the Aspergillus nidulans mitochondrial genome contains genes for arginine and asparagine tRNAs, an unassigned reading frame, and the structural gene for ATPase subunit 6. The tRNA genes possess 66% nucleotide homology and possibly originated by a relatively recent duplication event. The unassigned reading frame displays a low level of homology with the human URF A6L. The predicted amino acid sequence of the A-nidulans ATPase subunit 6 gene is 40% homologous to the yeast polypeptide and includes the short, highly conserved regions also present in the equivalent subunits from other mitochondrial systems and from Escherichia coli.

The mosaic organization of the apocytochrome b gene of Aspergillus nidulans revealed by DNA sequencing

The coding section of the apocytochrome b gene (cobA) of the mitochondrial DNA of Aspergillus nidulans has been completely sequenced. The gene comprises two exons of 507 and 654 bp separated by one intron of approximately 1.1 kb. The derived amino acid sequence shows 61% homology with that of Saccharomyces cerevisiae and 51% homology with the cognate human sequence. Comparison of these sequences indicates that UGA codes for tryptophan in the A. nidulans mitochondrial system. The intron is in exactly the same place as intron 13 of the apocytochrome b gene of "long" strains of S. cerevisiae. Other introns present in "long" strains (I1 and I2) are absent in A. nidulans. Introns 14 and 15 present both "long" and "short" strains of yeast are also absent. This is particularly significant in view of the involvement of 14 in the splicing of both cob and oxi3 (coding for cytochrome oxidase subunit 1) mRNA precursors in S. cerevisiae. The partial sequence of the A. nidulans intron shows an open reading frame for at least the first 200 bp, and shows the intron to be closed in all frames at the carboxyl terminus.

Conservation and rearrangement of mitochondrial structural gene sequences

Mitochondria contain the simplest DNA molecules that are present in eukaryotes. Mitochondrial DNA (mtDNA) is easily purified, and is an important model system for studying eukaryote gene structure and basic molecular processes. The protein sequences of mitochondrial gene products have been shown to be conserved from yeast to man, and there are definite similarities at the DNA sequence level. In contrast, the overall organization of the mitochondrial genome is drastically different in these organisms. To understand this, we need to extend work on mtDNA to a wider range of species. We have chosen to study the mtDNA of Aspergillus nidulans because a particularly comprehensive analysis of this system can be achieved using genetics as well as biochemistry, and like most eukaryotes it is an obligate aerobe, whereas Saccharomyces cerevisiae is not. We have investigated whether defined pieces of particular yeast mitochondrial genes show enough homology to Aspergillus mtDNA fragments to enable the corresponding Aspergillus genes to be located on the physical map. The results reported here show that this is the case for all five genes tested, and present the first data on the physical organization of the structural genes in the mitochondrial genome of A. nidulans.

Nuclear and mitochondrial suppression of a mitochondrially inherited cold-sensitive mutation in Aspergillus nidulans

Partial suppressors of a mitochondrially inherited mutation, [cs-67], conferring cold-sensitivity at 20 degrees C were identified. These mapped at one mitochondrial and four unlinked nuclear loci. Most suppressors partially restored the cytochrome aa3 deficiency of the cold-sensitive strain at 20 degrees C. Strains carrying two or more suppressors and [cs-67] showed considerably impaired growth. This effect was temperature-dependent, being more severe at 37 degrees C, and was not expressed in the presence of the [cs-67+] allele. The cytochrome oxidase activity of one of these strains was no more heat-sensitive than that of the wild-type implying that these mutations did not directly modify cytochrome oxidase. The wild-type strain grown in the presence of chloramphenicol and the cold-sensitive strain grown at 20 degrees C had similar cytochrome spectra and mitochondrial membrane protein profiles on sodium dodecyl sulphate gradient acrylamide gels. [cs-67] conferred pleiotropically a low level of resistance to paramomycin at 37 degrees C. It is suggested that [cs-67] and the suppressors act at the level of the mitochondrial ribosome.