Biomedical subjects

A Brennicke

Publications and source records attributed to A Brennicke.

At least 19 recordsLinked to original sources

PubMed1992

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed.

Amino Acid Sequence↗

PubMed1992

RNA editing in trans-splicing intron sequences of nad2 mRNAs in Oenothera mitochondria.

The complete open reading frame of subunit 2 of the NADH dehydrogenase in Oenothera mitochondria is split into five exons. The first two and the last three exons are encoded in distant genomic locations and are transcribed separately. Three tRNA genes coding for tRNA(Cys), tRNA(Asn), and tRNA(Tyr) are located upstream of the terminal three exons c, d, and e. The genomic distance, the interspersed tRNA genes, and the group II intron sequences flanking the two separated exons suggest trans-splicing to be required to connect exons b and c. Maturation of the mRNA includes RNA editing at 36 sites in the open reading frame. Three RNA editing events are observed in the split group II intron sequences. Two of these events allow after editing additional base pairings in the secondary structure, one in the stem of domain I, the other in the putative trans-pairing region of domain IV. These RNA editings may thus be involved in the trans-splicing reaction.

Amino Acid Sequence↗

PubMed1992

The nad4L gene is encoded between exon c of nad5 and orf25 in the Arabidopsis mitochondrial genome.

In the Arabidopsis thaliana mitochondrial genome the gene coding for subunit 4L of NADH dehydrogenase (nad4L) is located between exon c of the nad5 open reading frame and orf25. The physical proximity of these genes further supports the trans-splicing model for assembly of the nad5 mRNA. Some transcripts comprise the nad4L open reading frame cotranscribed with nad5 exon c and orf25, while other mRNAs contain only nad4L and orf25. Both open reading frames for nad4L and orf25 are edited in several positions with different frequencies.

Amino Acid Sequence↗

PubMed1992

The coxII gene in carrot mitochondria contains two introns.

The gene for cytochrome oxidase subunit II (coxII) in carrot is encoded by a unique locus in the mitochondrial genome. In contrast to the coxII genes in the numerous other plant species investigated to date, the coding region is interrupted by two group II introns. The carrot 5' intron is the homologue of the single intervening sequence found in several monocot and dicot coxII genes. Sequences similar to the 3' intron of the carrot coxII gene have not been reported previously and are not detectable by hybridization with Oenothera mtDNA. Northern hybridizations indicate complex precursor transcript patterns with mRNA molecules up to 10 kb length. The excised intron sequences appear to be stably maintained in the mRNA pool. Amino acid sequence comparisons suggest that the carrot coxII mRNA needs to be edited by numerous C to U transitions.

Amino Acid Sequence↗

PubMed1992

Regenerating good sense: RNA editing and trans splicing in plant mitochondria.

The protein products of plant mitochondrial genes cannot be predicted accurately from genomic sequences, since RNA editing modifies almost all mRNA sequences post-transcriptionally. Furthermore, RNA editing alters leader, trailer and intron sequences, and may be required for processing of these sequences. For several plant mitochondrial transcripts, processing includes trans splicing, which connects exons scattered throughout the genome. The mature transcripts are assembled via split group II intron sequences.

Introns↗

PubMed1991

RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria.

Amino Acid Sequence↗

PubMed1991

RNA editing in ATPase subunit 6 mRNAs in Oenothera mitochondria. A new termination codon shortens the reading frame by 35 amino acids.

The open reading frame encoding ATPase subunit 6 in Oenothera mitochondria is edited at 21 positions in all cDNA clones investigated. Only one of these events is silent, all others improve similarity between the homologous polypeptides of other species. The introduction of a new UAA termination codon shortens the polypeptide by 35 amino acids to a carboxy terminus conserved in other species. In one of the cDNA clones, an additional editing event was observed resulting in a premature UAA termination codon in the amino terminal region.

Adenosine Triphosphatases↗

PubMed1991

Nucleotide sequences of the mitochondrial genes trnS(TGA) encoding tRNA(TGASer) in Oenothera berteriana and Arabidopsis thaliana.

The genes encoding tRNA(TGASer) have been investigated in the mitochondrial (mt) genomes of Oenothera berteriana and Arabidopsis thaliana. Sequence analysis shows four nucleotide (nt) differences between the two dicots, but only two differences between each dicot and the available monocot sequences. Similarity comparisons identify these genes as encoding a native mt tRNA(TGASer), with less than 77% of the nt identical to the corresponding chloroplast tRNAs.

Base Sequence↗

PubMed1991

Trans splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences.

The complete NADH dehydrogenase subunit 1 (nad1) ORF in Oenothera mitochondria is encoded by five exons. These exons are located in three distant locations of the mitochondrial genome. One genomic region encodes exon a, the second encodes exons b and c, and the third specifies exons d and e. Cis-splicing group II introns separate exons b and c and d and e, while trans-splicing reactions are required to link exons a and b and c and d. The two parts of the group II intron sequences involved in these trans-splicing events can be aligned in domain IV. Exon sequences and the maturase-related ORF in intron d/e are edited by numerous C to U alterations in the mRNA. Two RNA editing events in the trans-splicing intron a/b improve conservation of the secondary structure in the stem of domain VI. RNA editing in intron sequences may thus be required for the trans-splicing reaction.

Amino Acid Sequence↗

PubMed1991

Trans splicing integrates an exon of 22 nucleotides into the nad5 mRNA in higher plant mitochondria.

The genes coding for NADH dehydrogenase subunit 5 (nad5) in mitochondria of the higher plants Oenothera and Arabidopsis are split into five exons that are located in three distant genomic regions. These encode exons a + b, c and d + e, respectively. Maturation of the mRNAs requires two trans splicing events to integrate exon c of only 22 nucleotides. Both trans splicing reactions involve mitochondrial group II intron sequences that allow base pairings in the interrupted domain IV, demonstrating the flexibility of intron structures. The observation of fragmented intron sequences in plant mitochondria suggests that trans splicing is more widespread than previously assumed. RNA editing by C to U alterations in both Oenothera and Arabidopsis open reading frames improves the evolutionary conservation of the encoded polypeptides. Three C to U RNA editing events were observed in intron sequences.

Amino Acid Sequence↗

PubMed1991

Distribution of RNA editing sites in Oenothera mitochondrial mRNAs and rRNAs.

To investigate whether RNA editing in plant mitochondria modifies structural RNAs as well as protein-coding RNAs we compared the genomic-encoded information with the respective transcripts of several genes in Oenothera. The genes analysed are the 5S, 18S and 26 S rRNAs, the alpha-subunit of ATPase (atpA), cytochrome b (cytb), orfB, which is located upstream of cytochrome oxidase subunit III, and the respective leader, trailer and spacer sequences. All open reading frames were found to be edited to some degree. The atpA coding region has the least edited mRNA in Oenothera mitochondria, with only four nucleotides altered in the 1533 nucleotide open reading frame. From this analysis we conclude that frequent RNA editing is indicative of functional protein coding regions in plant mitochondria. The extensive editing in orfB, for example, suggests that this orf codes for a mitochondrial protein. No RNA editing event was found in the 5S rRNA or in the 1824 nucleotides analysed of the 18S rRNA, but two nucleotides were found to be altered in the 1970 nucleotides compared for the 26S rRNA. One nucleotide alteration has changed C to U, the other in reverse U to C. However, only one of five cDNA clones covering this region shows the modifications, similar to many silent editing events in open reading frames. RNA editing in the structural RNAs thus does not seem to be essential for their function in the mitochondrial ribosome.

Adenosine Triphosphatases↗

PubMed1991

A mitochondrial intron sequence in the 5'-flanking region of a plant nuclear lectin gene.

A sequence fragment from the cis-splicing intron between exons a and b of the NADH-dehydrogenase subunit 5 gene (nad5) in plant mitochondria is also present in one of two closely related nuclear-encoded lectin genes of Dolichos biflorus. This sequence of 116 nucleotides is the major difference in the 5'-flanking region of two recently described lectin genes (Harada et al. 1990). The stem and leaf lectin DB58 does not contain the insert, while the otherwise more than 90% identical 5'-flanking region of the seed lectin is interrupted by this mitochondrial intron sequence.

Base Sequence↗

PubMed1990

RNA editing of ATPase subunit 9 transcripts in Oenothera mitochondria.

The mRNA for subunit 9 of the ATPase (atp9) in the higher plant Oenothera is edited in four nucleotide positions. Three events alter genomic serine and proline codons to triplets specifying leucine. A UGA termination codon is introduced into the reading frame by modification of a CGA arginine codon. This modification shortens the polypeptide by four amino acids. Direct sequencing of PCR amplified cDNA from the total mitochondrial mRNA population gives no indication of partially edited transcripts suggesting a rapid and efficient modification of atp9 transcripts in Oenothera mitochondria.

Amino Acid Sequence↗

PubMed1990

In vitro processing of mitochondrial and plastid derived tRNA precursors in a plant mitochondrial extract.

A lysate of purified mitochondria of the higher plant Oenothera processes in vitro synthesized tRNA precursors to the mature tRNA size. In vitro synthesized transcripts containing genuine plant mitochondrial tRNAs and analogous RNAs from mitochondrial loci with plastid derived tRNA sequences are accurately processed by an RNAase P-like activity to yield the mature 5'-terminus. A four nucleotide deletion in the anticodon stem-loop structure, however, prevents processing. The results show that in vitro transcripts containing tRNAs from sequence fragments of plastid origin integrated in plant mitochondrial genomes can be processed correctly in plant mitochondria, if tRNA sequences and structures are intact.

Base Sequence↗

PubMed1990

Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.

The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci.

Amino Acid Sequence↗

PubMed1990

Transcripts of the NADH-dehydrogenase subunit 3 gene are differentially edited in Oenothera mitochondria.

A number of cytosines are altered to be recognized as uridines in transcripts of the nad3 locus in mitochondria of the higher plant Oenothera. Such nucleotide modifications can be found at 16 different sites within the nad3 coding region. Most of these alterations in the mRNA sequence change codon identities to specify amino acids better conserved in evolution. Individual cDNA clones differ in their degree of editing at five nucleotide positions, three of which are silent, while two lead to codon alterations specifying different amino acids. None of the cDNA clones analysed is maximally edited at all possible sites, suggesting slow processing or lowered stringency of editing at these nucleotides. Differentially edited transcripts could be editing intermediates or could code for differing polypeptides. Two edited nucleotides in an open reading frame located upstream of nad3 change two amino acids in the deduced polypeptide. Part of the well-conserved ribosomal protein gene rps12 also encoded downstream of nad3 in other plants, is lost in Oenothera mitochondria by recombination events. The functional rps12 protein must be imported from the cytoplasm since the deleted sequences of this gene are not found in the Oenothera mitochondrial genome. The pseudogene sequence is not edited at any nucleotide position.

Amino Acid Sequence↗

PubMed1990

Species-specific RNA editing patterns in the mitochondrial rps13 transcripts of Oenothera and Daucus.

Transcripts from the rps13 locus, which encodes ribosomal protein S13, in Oenothera and Daucus mitochondria are edited by several cytidine to uridine transitions in both plants. Analysis of individual cDNA clones and polymerase chain reaction (PCR)-amplified cDNA from the total mitochondrial mRNA population shows different editing patterns in the two species. Although the same genomic triplet is conserved, nucleotides altered in the mRNA of one species are not necessarily edited in the other. Individual editing sites appear to be modified to varying degrees in the mRNA populations in both plant species, indicating that completely edited transcripts constitute only a minor fraction of the rps13 mRNA molecules.

Amino Acid Sequence↗

PubMed1990

Genes for tRNA(Gly), tRNA(His), tRNA(Lys), tRNA(Phe), tRNA(Ser) and tRNA(Tyr) are encoded in Oenothera mitochondrial DNA.

The genes coding for tRNA(Gly), tRNA(His), tRNA(Lys), tRNA(Phe), tRNA(Ser) and tRNA(Tyr) have been identified in Oenothera mitochondrial DNA. Sequence analysis of these genes and their surrounding sequences are presented and compared with other known tRNA genes from plant mitochondria. All six deduced tRNA sequences can be folded into the classical cloverleaf structure model. Only the tRNA(His) gene shows high homology with the corresponding chloroplast gene and thus appears to be derived from a transfer event of chloroplast sequences into the mitochondrial genome. The sequences surrounding this gene, however, show little similarity with the chloroplast genome. The other five deduced tRNAs display a much lower similarity with their chloroplast counterparts and thus appear to be genuine mitochondrial tRNAs. These tRNAs are highly conserved between monocots and dicots with maximally three nucleotides differing between the Oenothera sequences and their wheat homologues. A purine-rich sequence is found upstream of each tRNA gene in Oenothera, similar to wheat mitochondrial tRNA genes, that could be involved in transcription signalling.

Base Sequence↗