tRNA punctuation model of RNA processing in human mitochondria

Transcription and translation of mitochondrial DNA in interspecific somatic cell hybrids

We examined the mitochondrial transcription and translation products of somatic cell hybrids constructed by the fusion of Chinese hamster and mouse cells. The hybrid cell lines OAC-k, OAC-l, and OAC-m contain approximately equal amounts of hamster and mouse mitochondrial DNA and produced mitochondrial rRNA from both parental species in the same ratio. Cell lines OAC-k, OAC-l, and OAC-m also produced poly(A)+ mouse mitochondrial RNA transcripts comparable in complexity and quantity to poly(A)+ RNA from the mouse parent. However, the overall level of poly(A)+ hamster mitochondrial RNA from these hybrids was significantly reduced compared with that from the hamster parent. The hybrid cells also lacked several poly(A)+ RNA species found in the hamster parent, but contained additional minor transcripts. The mitochondrially coded proteins of the OAC-k, OAC-l, and OAC-m cells were predominantly encoded by the mouse mitochondrial DNA.

Mouse thymidylate synthase messenger RNA lacks a 3' untranslated region

Analysis of the sequence of cDNA corresponding to mouse thymidylate synthase (5,10-methylenetetrahydrofolate:dUMP C-methyltransferase, EC 2.1.1.45) mRNA revealed that the termination codon TAA was followed immediately by a poly(A) sequence. This raised the possibility that mouse thymidylate synthase mRNA lacks a 3' untranslated region. In the present study, we have further investigated this possibility. DNA corresponding to the 3' end of the thymidylate synthase gene was isolated from a genomic library. The sequence of the genomic DNA was identical to that of the cDNA in the coding region. However, the termination codon was TAG in the genomic sequence rather than TAA, and poly(A) was not present in the genomic DNA. Sequences flanking the site of poly(A) addition were in good agreement with polyadenylylation consensus sequences. S1 nuclease analysis revealed that approximately 80% of the thymidylate synthase mRNA molecules were polyadenylylated at the termination codon. A secondary polyadenylylation site was detected 190-200 nucleotides downstream of the primary site. We conclude that the major species of mouse thymidylate synthase mRNA lacks a 3' untranslated region and that the final A of the termination codon is added by poly(A) polymerase. It appears that a 3' untranslated region is not essential for the accumulation or translation of this mRNA.

Diverse patterns of expression of the cytochrome c oxidase subunit I gene and unassigned reading frames 4 and 5 during the life cycle of Trypanosoma brucei

Transcription of a maxicircle segment from Trypanosoma brucei 164 that contains nucleotide (nt) sequences corresponding to cytochrome c oxidase subunit I (COI) and unassigned reading frames (URFs) 4 and 5 of other mitochondrial systems was investigated. Two major transcripts that differ in size by ca. 200 nt map to each of the COI and URF4 genes, while a single major transcript maps to URF5. In total RNA, the larger COI transcript is more abundant in procyclic forms (PFs) than in bloodstream forms (BFs), the smaller COI and both URF4 transcripts have similar abundances in both forms, and the single URF5 transcript is more abundant in BF than PF. These patterns of expression differ in poly(A)+ RNA as a result of a higher proportion of poly(A)+ mitochondrial transcripts in PFs than in BFs. In addition, small (300- to 500-nt) RNAs that are transcribed from C-rich sequences located between putative protein-coding genes also exhibit diverse patterns of expression between life cycle stages and differences in polyadenylation in PFs compared with BFs. These observations suggest that multiple processes regulate the differential expression of mitochondrial genes in T. brucei.

The telomeres of the linear mitochondrial DNA of Tetrahymena thermophila consist of 53 bp tandem repeats

We have cloned and sequenced the telomeric DNA of the linear mitochondrial DNA (mtDNA) of T. thermophila BVII. The mtDNA telomeres consist of a 53 bp sequence tandemly repeated from 4 to 30 times, with most molecules having 15 +/- 4 repetitions. The previously recognized terminal heterogeneity of the mtDNA is completely accounted for by the variability in the number of repeats. The 53 bp repeat does not resemble known telomeric DNA in sequence, repeat size, or number of repetitions. The termini occur at heterogeneous positions within the 53 bp repeat. The junction of the telomeric repeat with the internal DNA is at a different position within the telomeric repeat on each end of the mtDNA. We propose a model for the maintenance of the mtDNA ends involving unequal homologous recombination.

Bovine cardiac mitochondrial ADP/ATP-carrier: two distinct mRNAs and an unusually short 3'-noncoding sequence

cDNA clones for bovine cardiac mitochondrial ADP/ATP carrier have been isolated. They hybridize with two mRNAs that differ in size by about 300 nucleotides. The concentration ratio and total abundance of the two mRNAs varies among bovine tissues (heart, liver, kidney, and uterus). At least one of them has an unusually short 3'-noncoding sequence, which includes the two consensus cleavage/polyadenylation signal sequences CATTG and ATTAAA. The 3'-end shows complementarity to regions of human U4 small nuclear RNA. The predicted amino acid sequence confirms the reported sequence from Val207 to the C-terminal Val297, which has been proposed (residue 279-291) to contribute to a nucleotide binding site.

RNA mapping on Drosophila mitochondrial DNA: precursors and template strands

Drosophila melanogaster mitochondrial DNA (mtDNA) is closely related to the mammalian and amphibian mtDNA except for gene organization. In Drosophila, genes are distributed in clusters alternatively coded on each strand. Besides the eleven major foreseeable transcripts previously described (MERTEN and PARDUE, 1981, J. Mol. Biol., 153, 1-21), we have characterized two poly A+ transcripts, one major and one minor which could correspond respectively to the ND3 and ND6 reading frames, and 27 poly A+ minor transcripts (0.2 to greater than 3.2 kb) which are distributed along the mtDNA except in the rRNAs, ND 1 and A+ T rich regions. The mapping and length of 25 of these transcripts strongly suggest a precursor role. They would be processed at the level of tRNA or tRNA-like sequences. Most of them are transcribed from the template strand of each gene cluster and their distribution is in agreement with the hypothesis of several transcription origins and terminations located near the extremities of each gene cluster. Quantitatively our results show a large variation in each presumptive mature transcript compared to the other, even in a given gene cluster, suggesting a specific degradation of some of the mature transcripts.

Transcription and translation of mitochondrial DNA in interspecific somatic cell hybrids

We examined the mitochondrial transcription and translation products of somatic cell hybrids constructed by the fusion of Chinese hamster and mouse cells. The hybrid cell lines OAC-k, OAC-l, and OAC-m contain approximately equal amounts of hamster and mouse mitochondrial DNA and produced mitochondrial rRNA from both parental species in the same ratio. Cell lines OAC-k, OAC-l, and OAC-m also produced poly(A)+ mouse mitochondrial RNA transcripts comparable in complexity and quantity to poly(A)+ RNA from the mouse parent. However, the overall level of poly(A)+ hamster mitochondrial RNA from these hybrids was significantly reduced compared with that from the hamster parent. The hybrid cells also lacked several poly(A)+ RNA species found in the hamster parent, but contained additional minor transcripts. The mitochondrially coded proteins of the OAC-k, OAC-l, and OAC-m cells were predominantly encoded by the mouse mitochondrial DNA.

Nucleotide sequence of the bacteriophage T5 DNA fragment which contains the gene for tRNAAsp

The nucleotide sequence of bacteriophage T5 tRNAAsp has been determined by conventional methods using thin-layer chromatography on cellulose for oligonucleotide fractionation. It exhibits several unusual features, such as (a) the displacement of the constant residues U-8, A-14 and R-15; (b) the presence of three G X U out of four base pairs in the D-stem. The gene for T5 tRNAAsp has been cloned in pBR 322 and sequenced. The analysis of the flanking regions shows the presence of two open reading frames on both sides of this gene. It has also been shown that the cloned gene is expressed in Escherichia coli, and RNase P is involved in the T5 tRNAAsp processing.

The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code

The sequence of the 16,019 nucleotide-pair mitochondrial DNA (mtDNA) molecule of Drosophila yakuba is presented. This molecule contains the genes for two rRNAs, 22 tRNAs, six identified proteins [cytochrome b, cytochrome c oxidase subunits I, II, and III (COI-III), and ATPase subunits 6 and 8] and seven presumptive proteins (URF1-6 and URF4L). Replication originates within a region of 1077 nucleotides that is 92.8% A + T and lacks any open reading frame larger than 123 nucleotides. An equivalent to the sequence found in all mammalian mtCDNAs that is associated with initiation of second-strand DNA synthesis is not present in D. yakuba mtDNA. Introns are absent from D. yakuba mitochondrial genes and there are few (0-31) intergenic nucleotides. The genes found in D. yakuba and mammalian mtDNAs are the same, but there are differences in their arrangement and in the relative proportions of the complementary strands of the molecule that serve as templates for transcription. Although the D. yakuba small and large mitochondrial rRNA genes are exceptionally low in G and C and are shorter than any other metazoan rRNA genes reported, they can be folded into secondary structures remarkably similar to the secondary structures proposed for mammalian mitochondrial rRNAs. D. yakuba mitochondrial tRNA genes, like their mammalian counterparts, are more variable in sequence than nonorganelle tRNAs. In mitochondrial protein genes ATG, ATT, ATA, and in one case (COI) ATAA appear to be used as translation initiation codons. The only termination codon found in these genes is TAA. In the D. yakuba mitochondrial genetic code, AGA, ATA, and TGA specify serine, isoleucine, and tryptophan, respectively. Fifty-nine types of sense condon are used in the D. yakuba mitochondrial protein genes, but 93.8% of all codons end in A or T. Codon-anticodon interactions may include both G-A and C-A pairing in the wobble position. Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in the D. yakuba mtDNA molecule where these nucleotides are compatible with function.

Diverse patterns of expression of the cytochrome c oxidase subunit I gene and unassigned reading frames 4 and 5 during the life cycle of Trypanosoma brucei

Transcription of a maxicircle segment from Trypanosoma brucei 164 that contains nucleotide (nt) sequences corresponding to cytochrome c oxidase subunit I (COI) and unassigned reading frames (URFs) 4 and 5 of other mitochondrial systems was investigated. Two major transcripts that differ in size by ca. 200 nt map to each of the COI and URF4 genes, while a single major transcript maps to URF5. In total RNA, the larger COI transcript is more abundant in procyclic forms (PFs) than in bloodstream forms (BFs), the smaller COI and both URF4 transcripts have similar abundances in both forms, and the single URF5 transcript is more abundant in BF than PF. These patterns of expression differ in poly(A)+ RNA as a result of a higher proportion of poly(A)+ mitochondrial transcripts in PFs than in BFs. In addition, small (300- to 500-nt) RNAs that are transcribed from C-rich sequences located between putative protein-coding genes also exhibit diverse patterns of expression between life cycle stages and differences in polyadenylation in PFs compared with BFs. These observations suggest that multiple processes regulate the differential expression of mitochondrial genes in T. brucei.

Expression of the cytochrome b-URF6-URF5 region of the mouse mitochondrial genome

The nature of RNA coded by the only light-strand (L-strand) open-reading frame unidentified reading frame 6 (URF6) was studied by using a variety of single- and double-strand DNA subclones derived from the 3.6-kilobase (kb) cytochrome b (cyt b)-URF5 coding region of the mouse mitochondrial genome. Northern blot experiments using single-strand-specific M13 clones indicate that both the heavy (H) and L strands of this genomic region are symmetrically transcribed and processed into poly(adenylic acid) [poly(A)] RNAs of comparable size. The 1.2- and 2.4-kb RNAs coded by the H strand, putative mRNAs for cyt b and URF5 reading frames, respectively, are derived from a common precursor of 3.6-kb RNA. The L-strand-coded 1.15-kb RNA, on the other hand, is derived from a short-lived precursor of 3.6-kb RNA by a multiple-step processing involving a 2.4-kb intermediate RNA. The S1 nuclease protection experiments using both the 3'- or 5'-end-labeled DNA probes and also affinity-purified 32P-labeled RNA probes indicate that the 1.15-kb RNA maps between the start of the URF6 reading frame (3' end) and a region 590-600 nucleotides to the 5' end of this reading frame. The 1.15-kb RNA thus contains the entire URF6 coding sequence and an about 590-nucleotide-long 3' untranslated region. The molar abundance of the three mRNAs in the steady-state mitochondrial RNA varies markedly. The 1.15-kb URF6 mRNA is only one-tenth the level of 1.2-kb cyt b mRNA, although it is nearly as abundant as the 2.4-kb URF5 mRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of the polypeptide encoded by the URF-1 gene of Neurospora crassa mtDNA

Two peptides, potentially representing antigenic determinants of a proposed gene product, were synthesized. The peptide sequences were deduced from the nucleotide sequence of the unidentified reading frame (URF)1 of the Neurospora crassa mitochondrial genome. Specific antisera to the synthetic peptides were produced. The antibodies recognized a single polypeptide species with an apparent relative molecular mass of about 30 000. The mitochondrial origin of this polypeptide was verified by in vivo labelling experiments in the presence of cycloheximide, as well as by in vitro translation using isolated mitochondria. The chemical identification of the protein was performed by partial radiosequencing of the N-terminal portion of the immunoprecipitated URF-1 product. The amount of URF-1 polypeptide present in N. crassa mitochondria is in the range of 1-2%. The protein is a constituent of the inner envelope of the organelle and probably part of a more complex membrane unit.

Apocytochrome b and other mitochondrial DNA sequences are differentially expressed during the life cycle of Trypanosoma brucei

Cytochromes and Krebs cycle enzymes are not detected in bloodstream forms of Trypanosoma brucei but are present in procyclic forms. We have analyzed transcription of mitochondrial sequences which contain the apocytochrome b gene and several other open reading frames (ORFs). Multiple transcripts map to individual DNA sequences located on both DNA strands. Larger low abundance transcripts map to multiple ORFs and may be precursor RNAs. Small abundant transcripts map to G + C rich sequences that do not have obvious protein coding functions. The larger of two presumptive apocytochrome b transcripts is strikingly more abundant in procyclic than bloodstream forms and other mitochondrial transcripts are also differentially abundant between these two forms. In addition, many mitochondrial transcripts appear to be differentially polyadenylated between bloodstream and procyclic forms. We suggest that the mechanisms which regulate the production of the mitochondrial respiratory system in T. brucei involve differential expression of mitochondrial genes.

Identification of an aspartate transfer RNA gene in maize mitochondrial DNA

A gene for a transfer RNA (tRNA) specific for aspartic acid was identified in maize mitochondrial DNA. The nucleotide sequence and predicted secondary structure of this tRNA more closely resemble eubacterial and chloroplast aspartate tRNA genes than other mitochondrial aspartate tRNA genes. This gene is located on a 3,123 base pair EcoRI DNA fragment that also contains an elongator methionine tRNA gene. These two tRNA genes are separated by 726 nucleotides and are located on opposite strands of DNA.

The wheat mitochondrial gene for apocytochrome b: absence of a prokaryotic ribosome binding site

The wheat mitochondrial gene for apocytochrome b (CYB) has been identified by its hybridization to a yeast CYB probe and its nucleotide sequence has been determined. The wheat CYB sequence predicts a cytochrome b apoprotein of 398 amino acids; it is almost identical to that of maize but has ten additional amino acids at the carboxy terminus. No introns are present in the wheat CYB gene, but an internal segment of the gene is repeated at another genomic location. Transcript analysis reveals a single wheat CYB mRNA of approximately 2.4 kb with a long untranslated leader. Sequences upstream of the CYB coding region are very similar in wheat and maize but the stretch proposed to be a ribosome binding site in maize is not conserved in wheat. The corresponding leader regions of the wheat mitochondrial mRNAs for cytochrome oxidase subunits I and II also lack complementarity to the 3'-end of the small subunit rRNA. We conclude that alternative signals are involved in the initiation of translation in plant mitochondria.

The 3' end of large ribosomal subunit RNA from mosquito mitochondria: homogeneity of transcribed moieties

3' Terminal sequences of mosquito mitochondrial 16 S ribosomal RNA, which is post-transcriptionally polyadenylated, have been examined with the aim of determining the degree of homogeneity of transcribed moieties. 3' End-labeled samples were subjected to oligonucleotide fingerprint analysis and to ladder gel analysis after primary and secondary nuclease digestion; and products of reverse transcriptase reactions were characterized using 16 S RNA as template and selected oligodeoxynucleotides as primers. The results indicated a remarkable degree of homogeneity compared to homologous mammalian mitochondrial systems, and suggested differences in modes of expression of insect, versus mammalian, mitochondrial genomes.

Distribution of transfer RNA genes in thePisum sativum chloroplast DNA

Purified chloroplast tRNAs were isolated fromPisum sativum leaves and radioactively labeled at their 3' end using tRNA nucleotidyl transferase and α(32)P-labeled CTP. Pea ctDNA was fragmented using a number of restriction endonucleases and hybridized with thein vitro labeled chloroplast tRNAs by DNA transfer method. Genes for tRNAs have been found to be dispersed throughout the chloroplast genome. A closer analysis of the several hybrid regions using recombinant DNA plasmids have shown that tRNA genes are localized in the chloroplast genome in both single and multiple arrangements. Two dimensional gel electrophoresis of total ct tRNA have identified 36 spots. All of them have been found to hybridize withPisum sativum ctDNA. Using recombinant clones, 30 of the tRNA spots have been mapped inPisum sativum ctDNA.

A study of mitochondrial and nuclear transcription with cloned cDNA probes. Changes in the relative abundance of mitochondrial transcripts after stimulation of quiescent mouse fibroblasts

From a cDNA library constructed in pBR322 we have isolated and studied a set of clones corresponding to mRNAs whose abundance changes when serum-deprived murine fibroblasts are stimulated to enter the cell cycle. A subset of these clones was derived from mRNA species whose abundance decreased during the G1 period following serum stimulation; all but one of these clones turned out to be clones of mitochondrial poly(A)mRNAs. There was no detectable change in the rate of transcription of the mitochondrial genome compared with the nuclear genome, and the lengths of the poly(A) segments on both mRNA species did not change significantly after serum stimulation. We conclude that the apparent decline in the relative abundance of the mitochondrial mRNAs is the result of a relative increase in the processing and/or transport of nuclear mRNA.

Polyadenylation of a human mitochondrial ribosomal RNA transcript detected by molecular cloning

We have identified by molecular cloning a polyadenylated RNA transcript in the human leukemia cell line, K562, which is complementary to a portion of the gene-encoding mitochondrial 16S ribosomal RNA (mt 16S rRNA). The cloned portion of the transcript corresponds to positions 2191-2395 of the human mt genome. The clone represents a cDNA copy of an RNA transcript from the H strand and carries an additional poly(A) tail 21 residues long at its 3'-end. Our data provide direct evidence for polyadenylation of some mt 16S rRNA transcripts.

Highly efficient RNA-synthesizing system that uses isolated human mitochondria: new initiation events and in vivo-like processing patterns

A highly efficient RNA-synthesizing system with isolated HeLa cell mitochondria has been developed and characterized regarding its requirements and its products. In this system, transcription is initiated and the transcripts are processed in a way which closely reproduces the in vivo patterns. Total RNA labeling in isolated mitochondria proceeds at a constant rate for about 30 min at 37 degrees C; the estimated rate of synthesis is at least 10 to 15% of the in vivo rate. Polyadenylation of the mRNAs is less extensive in this system than in vivo. Furthermore, compared with the in vivo situation, rRNA synthesis in vitro is less efficient than mRNA synthesis. This is apparently due to a decreased rate of transcription initiation at the rRNA promoter and probably a tendency also for premature termination of the nascent rRNA chains. The 5'-end processing of rRNA also appears to be slowed down, and it is very sensitive to the incubation conditions, in contrast to mRNA processing. It is suggested that the lower efficiency and the lability of rRNA synthesis and processing in isolated mitochondria may be due to cessation of import from the cytoplasm of ribosomal proteins that play a crucial role in these processes. The formation of the light-strand-coded RNA 18 (7S RNA) is affected by high pH or high ATP concentration differently from the overall light-strand transcription. The dissociation of the two processes may have important implications for the mechanism of formation and the functional role of this unusual RNA species. The high efficiency, initiation capacity, and processing fidelity of the in vitro RNA-synthesizing system described here make it a valuable tool for the analysis of the role of nucleocytoplasmic-mitochondrial interactions in organelle gene expression.

Highly efficient RNA-synthesizing system that uses isolated human mitochondria: new initiation events and in vivo-like processing patterns

A highly efficient RNA-synthesizing system with isolated HeLa cell mitochondria has been developed and characterized regarding its requirements and its products. In this system, transcription is initiated and the transcripts are processed in a way which closely reproduces the in vivo patterns. Total RNA labeling in isolated mitochondria proceeds at a constant rate for about 30 min at 37 degrees C; the estimated rate of synthesis is at least 10 to 15% of the in vivo rate. Polyadenylation of the mRNAs is less extensive in this system than in vivo. Furthermore, compared with the in vivo situation, rRNA synthesis in vitro is less efficient than mRNA synthesis. This is apparently due to a decreased rate of transcription initiation at the rRNA promoter and probably a tendency also for premature termination of the nascent rRNA chains. The 5'-end processing of rRNA also appears to be slowed down, and it is very sensitive to the incubation conditions, in contrast to mRNA processing. It is suggested that the lower efficiency and the lability of rRNA synthesis and processing in isolated mitochondria may be due to cessation of import from the cytoplasm of ribosomal proteins that play a crucial role in these processes. The formation of the light-strand-coded RNA 18 (7S RNA) is affected by high pH or high ATP concentration differently from the overall light-strand transcription. The dissociation of the two processes may have important implications for the mechanism of formation and the functional role of this unusual RNA species. The high efficiency, initiation capacity, and processing fidelity of the in vitro RNA-synthesizing system described here make it a valuable tool for the analysis of the role of nucleocytoplasmic-mitochondrial interactions in organelle gene expression.

Sequence and arrangement of the genes for cytochrome b, URF1, URF4L, URF4, URF5, URF6 and five tRNAs in Drosophila mitochondrial DNA

The nucleotide sequence of a segment of the mtDNA molecule of Drosophila yakuba has been determined, within which have been identified the 3' end of the large rRNA gene and the entire genes for tRNAleuCUN , URF1 , tRNAserUCN , cytochrome b, URF6 , tRNApro, tRNAthr , URF4L , URF4 , tRNAhis and URF5 . The genes are arranged in the order given, with the large rRNA gene being closest to the A+T-rich region which contains the origin of replication. Transcription of all of these genes except those for cytochrome b, URF6 , tRNAserUCN and tRNAthr proceeds in the same direction as replication. Differences occur in the relative arrangement and in the direction of transcription of these twelve genes between D. yakuba and mammalian mtDNA molecules. Internal AGA codons occur in all of the polypeptide genes except URF6 . Comparisons of the positions of these AGA codons to codons in corresponding mouse genes is consistent with the view that in the D. yakuba mitochondrial genetic code AGA specifies serine. Genes equivalent to all of the polypeptide, tRNA and rRNA genes found in mammalian mtDNA have now been identified in D. yakuba mtDNA.

Optimization of in vitro protein synthesis by isolated mouse adrenal mitochondria

The requirements for in vitro mitochondrial protein synthesis have been studied using isolated mitochondria from cultured adrenal Y-1 tumor cells from mice. By reducing the reaction volume to 50 microliter we were able to assay in replicate the requirements for various reaction components using trichloroacetic acid (TCA)-precipitable counts for a quantitative evaluation with time of incubation. Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis followed by autoradiography was also used for a qualitative and quantitative evaluation of the translation products. With the optimized system, 1 to 3% of added [35S]methionine was incorporated. The products of mitochondrial protein synthesis range from 70,000 to 5000 molecular weight. Major autoradiographic bands were observed at 38,000, 31,000, 23,000, 20,000, and 5600 molecular weight as separated on 10 to 20% gradient SDS-polyacrylamide gels; however, 20 to 30 protein products of various molecular weights were discernible. Mitochondrial concentrations of 0.8 to 1.4 mg/ml of incubation gave the better incorporation of [35S]methionine per milligram of protein. Total [35S]methionine incorporated into mitochondrial protein was greatest at 25 degrees C after 90 min. Chloramphenicol at 10 micrograms/ml inhibited mitochondrial protein synthesis by more than 50% and at 100 micrograms/ml inhibited incorporation by more than 95%. Cycloheximide had no effect on incorporation at less than 1.0 mg/ml. Magnesium and ATP in a molar ratio of one to one at 5 mM gave optimal incorporation. Other energy generating systems using oxidative phosphorylation to supply ATP for protein synthesis were not as effective as ATP and 5 mM phosphoenol pyruvate, 20 micrograms/ml pyruvate kinase and 5 mM a-ketoglutarate. In contrast to in vitro yeast mitochondrial protein synthesis, no enhancement of in vitro adrenal cell mitochondrial protein synthesis was found with GTP or its analogs. The buffers N,N-bis(2-hydroxyethyl)glycine, N-(tris(hydroxymethyl)methyl)glycine, and N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid were superior to Tris-HCl for mitochondrial protein synthesis. Optimal pH for [35S]methionine incorporation into mitochondrial proteins was pH 7.0 to 7.6. Potassium at 50 to 90 mM gave the best incorporation of [35S]methionine, and the higher molecular weight products of translation were enhanced at these concentrations. Sodium at 10 to 40 mM had no effect; however, 100 mM sodium inhibited label incorporation by 30%. Calcium at 100 microM inhibited mitochondrial protein synthesis by approximately 50%, and at 1.0 mM little if any incorporation occurred.(ABSTRACT TRUNCATED AT 400 WORDS)

A cluster of six tRNA genes in Drosophila mitochondrial DNA that includes a gene for an unusual tRNAserAGY

Genes for URF3, tRNAala, tRNAarg, tRNAasn, tRNAserAGY, tRNAglu, tRNAphe, and the carboxyl terminal segment of the URF5 gene have been identified within a sequenced segment of the mtDNA molecule of Drosophila yakuba. The genes occur in the order given. The URF5 and tRNAphe genes are transcribed in the same direction as replication while the URF3 and remaining five tRNA genes are transcribed in the opposite direction. Considerable differences exist in the relative arrangement of these genes in D. yakuba and mammalian mtDNA molecules. In the tRNAserAGY gene an eleven nucleotide loop, within which secondary structure formation seems unlikely, replaces the dihydrouridine arm, and both the variable loop (six nucleotides) and the T phi C loop (nine nucleotides) are larger than in any other D. yakuba tRNA gene. As available evidence is consistent with AGA codons specifying serine rather than arginine in the Drosophila mitochondrial genetic code, the possibility is considered that the 5'GCU anticodon of the D. yakuba tRNAserAGY gene can recognize AGA as well as AGY codons.

The nucleotide sequence of a segment of Trypanosoma brucei mitochondrial maxi-circle DNA that contains the gene for apocytochrome b and some unusual unassigned reading frames

The nucleotide sequence of a 2.5-kb segment of the maxi-circle of Trypanosoma brucei mtDNA has been determined. The segment contains the gene for apocytochrome b, which displays about 25% homology at the amino acid level to the apocytochrome b gene from fungal and mammalian mtDNAs. Northern blot and S1 nuclease analyses have yielded accurate map positions of an RNA species in an area that coincides with the reading frame. The segment also contains two pairs of overlapping unassigned reading frames, which lack homology with any known mitochondrial gene or URF. The DNA sequence in these areas is AG-rich (70%), resulting in URFs with an unusually high level of glycine and charged amino acids (60%). They may not encode proteins, in spite of their size and the fact that abundant transcripts are mapped in these areas.

Genes for cytochrome c oxidase subunit I, URF2, and three tRNAs in Drosophila mitochondrial DNA

Genes for URF2, tRNAtrp, tRNAcys, tRNAtyr and cytochrome c oxidase subunit I (COI) have been identified within a sequenced segment of the Drosophila yakuba mtDNA molecule. The five genes are arranged in the order given. Transcription of the tRNAcys and tRNAtyr genes is in the same direction as replication, while transcription of the URF2, tRNAtrp and COI genes is in the opposite direction. A similar arrangement of these genes is found in mammalian mtDNA except that in the latter, the tRNAala and tRNAasn genes are located between the tRNAtrp and tRNAcys genes. Also, a sequence found between the tRNAasn and tRNAcys genes in mammalian mtDNA, which is associated with the initiation of second strand DNA synthesis, is not found in this region of the D. yakuba mtDNA molecule. As the D. yakuba COI gene lacks a standard translation initiation codon, we consider the possibility that the quadruplet ATAA may serve this function. As in other D. yakuba mitochondrial polypeptide genes, AGA codons in the URF2 and COI genes do not correspond in position to arginine-specifying codons in the equivalent genes of mouse and yeast mtDNAs, but do most frequently correspond to serine-specifying codons.

Identification of the polypeptides encoded in the ATPase 6 gene and in the unassigned reading frames 1 and 3 of human mtDNA

Antibodies prepared against chemically synthesized peptides predicted from the DNA sequence have been used to identify the polypeptides encoded in the ATPase 6 gene and in unidentified reading frames (URFs) 1 and 3 of human mtDNA. In particular, antibodies directed against the COOH-terminal nonapeptide of the putative polypeptide encoded in the ATPase 6 reading frame immunoprecipitated specifically component 17 of the HeLa cell mitochondrial translation products, the reaction being inhibited by the specific peptide. Similarly, antibodies directed against the COOH-terminal undecapeptide of the putative URF1 product or against the COOH-terminal heptapeptide of the presumptive URF3 product were effective in immunoprecipitating specifically component 12 or, respectively, component 24 of the mitochondrial translation products. The sizes of proteins 17, 12, and 24, as estimated from their electrophoretic mobilities, are compatible with their being the products of the ATPase 6 gene, URF1, and URF3, respectively.

Repeated sequences and open reading frames in the 3' flanking region of the gene for the RNA subunit of Escherichia coli ribonuclease P

We have determined the identity of about 700 nucleotides in the 3' flanking region of the gene for M1 RNA, the RNA component of RNase P (EC 3.1.26.5). This region begins with a 113-base-pair segment of DNA, which is repeated approximately 3.5 times. The first repeating unit originates within the gene sequence for the 3' end of mature M1 RNA. The repeating units are highly conserved but diverge considerably after the partial fourth repeat. Segments of sequence homologous to the repeats have been identified both upstream in the M1 RNA transcription unit and downstream from the repeating units. Several overlapping open reading frames, with the potential to encode small basic proteins, have been identified in the repeated sequences. The structure of the M1 RNA gene 3' flanking region is very similar to the corresponding region at the Tyr T locus. In vitro and in vivo, transcription of the M1 RNA gene appears to terminate about 40 nucleotides downstream from the 3' terminus of mature M1 RNA. Therefore, an RNA processing event is involved in the biosynthesis of M1 RNA.

The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units

A detailed analysis of the mapping and kinetic properties of oligo(dT)-cellulose bound and unbound transcripts synthesized in HeLa cells has indicated that two distinct transcription events take place in the rDNA region. Of these, one appears to start approximately 25 bp upstream of the tRNAPhe gene and to terminate at or near the 3' end of the 16S rRNA gene, being responsible for the synthesis of the bulk of rRNA. The other transcription event starts near the 5' end of the 12S rRNA gene, proceeds beyond the 3' end of the 16S rRNA gene, and results in the synthesis of a polycistronic molecule corresponding to almost the entire H-strand, which is destined to be processed to yield the mRNAs and most of the tRNAs encoded in the heavy strand. The existence of two overlapping transcription units with distinct promoters is probably the basis for the differential regulation of synthesis of the rRNAs and heavy-strand-coded mRNAs.

Discrete poly(A)- RNA species from rat liver mitochondria are fragments of 16S mitochondrial rRNA carrying its 5'-termini

During electrophoresis in polyacrylamide gels containing 7M urea the major discrete components of preparations of rat liver mitochondrial poly(A)+ and poly(A)- RNA species have similar mobilities. Poly(A)- RNA components hybridize to the 16S rRNA gene of mtDNA. Analysis of 5'-terminal sequences of these components revealed their identity to the 5'-terminal sequence of 16S rRNA. These results show that poly(A)- RNA components are fragmentation products of 16S rRNA. Fragmentation occurs nonrandomly from the 3'-end of the original rRNA molecules and lead to formation of products with electrophoretic mobilities similar to those of poly(A)+ RNA components.

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.

Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code

The sequence of a 4,869 base-pair fragment of Drosophila melanogaster mitochondrial DNA is presented. It contains genes for cytochrome oxidase subunits I, II and III, ATPase subunit 6 and six tRNAs together with two unassigned reading frames. The gene organization differs from that of mammalian mitochondrial DNAs. Evidence is provided for a genetic code in which AGA codes for serine and the quadruplet ATAA is used in initiation of translation.

Biogenesis of mitochondria: the mitochondrial gene (aap1) coding for mitochondrial ATPase subunit 8 in Saccharomyces cerevisiae

A mitochondrial gene (denoted aap1) in Saccharomyces cerevisiae has been characterized by nucleotide sequence analysis of a region of mtDNA between the oxi3 and oli2 genes. The reading frame of the aap1 gene specifies a hydrophobic polypeptide containing 48 amino acids. The functional nature of this reading frame was established by sequence analysis of a series of mit- mutants and revertants. Evidence is presented that the aap1 gene codes for a mitochondrially synthesized polypeptide associated with the mitochondrial ATPase complex. This polypeptide (denoted subunit 8) is a proteolipid whose size has been previously assumed to be 10 kilodaltons based on its mobility on SDS-polyacrylamide gels, but the sequence of the aap1 gene predicts a molecular weight of 5,815 for this protein.

Nucleotide sequence of a segment of Drosophila mitochondrial DNA that contains the genes for cytochrome c oxidase subunits II and III and ATPase subunit 6

The nucleotide sequence of a segment of the mtDNA molecule of Drosophila yakuba has been determined, within which have been identified the genes for tRNAleuUUR, cytochrome c oxidase subunit II (COII), tRNAlys, tRNAasp, URFA6L, ATPase subunit 6 (ATPase6), cytochrome c oxidase subunit III (COIII) and tRNAgly. The genes are arranged in the order given and all are transcribed from the same strand of the molecule in a direction opposite to that in which replication proceeds around the molecule. The tRNAlys gene is unusual among mitochondrial tRNAlys genes in that it contains a CTT anticodon. The triplet AGA is used to specify an amino acid in all of the COII, COIII, ATPase6, and URFA6L genes. However, the AGA codons found in these four polypeptide genes correspond in position to codons which specify nine different amino acids, but never arginine, in the equivalent polypeptide gene which have been sequenced from mtDNAs of mouse, yeast and Zea mays.

Transfer RNA genes in Drosophila mitochondrial DNA: related 5' flanking sequences and comparisons to mammalian mitochondrial tRNA genes

Genes for tRNAgly and tRNAserUCN have been identified within sequences of mtDNA of Drosophila yakuba. The tRNAgly gene lies between the genes for cytochrome c oxidase subunit III and URF3, and all three of these genes are contained in the same strand of the mtDNA molecule. The tRNAserUCN gene is adjacent to the URF1 gene. These genes are contained in opposite strands of the mtDNA molecule and their 3' ends overlap. The structures of the tRNAgly and tRNAserUCN genes, and of the four tRNA genes of D. yakuba mtDNA reported earlier (tRNAile, tRNAgln, tRNAf-met and tRNAval) are compared to each other, to non-organelle tRNAs, and to corresponding mammalian mitochondrial tRNA genes. Within 19 nucleotides upstream from the 5' terminal nucleotide of each of the Drosophila mitochondrial tRNAgly, tRNAserUCN, tRNAile, tRNAgln and tRNAf-met genes occurs the sequence 5'TTTATTAT, or a sequence differing from it by one nucleotide substitution. Upstream from this octanucleotide sequence, and separated from it by 3, 4 and 11 nucleotides, respectively, in the 5' flanking regions of the tRNAile, tRNAserUCN and tRNAgly genes occurs the sequence 5'GATGAG.

Antibodies against synthetic peptides reveal that the unidentified reading frame A6L, overlapping the ATPase 6 gene, is expressed in human mitochondria

Antibodies prepared against chemically synthesized peptides predicted from the DNA sequence have been used to detect human mitochondrial gene products. In particular, antibodies directed against either the NH2-terminal decapeptide or the COOH-terminal undecapeptide of cytochrome c oxidase subunit II (COII) were both very effective in immunoprecipitating the previously identified COII polypeptide from an SDS lysate of mitochondria from HeLa cells. Similarly, antibodies directed against the COOH-terminal nonapeptide of the putative polypeptide encoded in the unidentified reading frame A6L, which overlaps the ATPase 6 gene, immunoprecipitated specifically a component (#25) of the HeLa cell mitochondrial translation products; antibodies directed against the NH2-terminal octapeptide also precipitated protein 25, although less efficiently. The size of protein 25, as estimated from its electrophoretic mobility, is compatible with its being the unidentified reading frame A6L product. Furthermore, a fingerprinting analysis of this protein after trypsin digestion has given results consistent with this identification.