The two human organic cation transporter genes SLC22A1 and SLC22A2 are located on chromosome 6q26

Polyspecific transporters for organic cations (OCT) belong to a new protein family which also include organic anion transporters. The first human transporters from this family (OCT1, OCT2) have been recently cloned. They translocate small cations like tetraethylammonium, choline and monoamine neurotransmitters and are involved in hepatic and renal cation excretion, respectively. We have localized the OCT1 and OCT2 genes (SLC22A1, SLC22A2) on chromosome 6q26.

Cloning, chromosomal localization and functional expression of the gene encoding the alpha-subunit of the cGMP-gated channel in human cone photoreceptors

Cyclic nucleotide-gated (CNG) ion channels serve as final targets of signal transduction in vertebrate photoreceptors. While the basic mechanisms of phototransduction are similar in rod and cone photoreceptors, both cell types express distinct sets of components of the transduction pathway. We report here the cloning of the cDNA encoding the alpha-subunit of the cGMP-gated channel of human cone photoreceptors. The open reading frame predicts a polypeptide of 694 amino acid residues with conserved functional parts and amino acid positions typical for the alpha-subunit of CNG-channels. Heterologous expression of the cDNA in Xenopus oocytes gave rise to cGMP-gated channel activity. Antiserum directed against the C-terminus of the bovine cone CNG channel alpha-subunit crossreacted specifically with the heterologously expressed polypeptide and stained cone photoreceptors and weakly also the outer plexiform layer in human retinal sections. Northern blot analysis detected a prominent mRNA species of approximately 3.8 kb in human retina. The entire gene spans approximately 30 kb of genomic sequence and is located on the pericentric band q11.2 of human chromosome 2. The gene is composed of seven exons, with introns located at positions which are preserved with respect to the human rod gene, indicating a common ancestral gene structure. RT-PCR analysis gave no evidence for alternatively spliced transcripts.

RDS/peripherin gene mutations are frequent causes of central retinal dystrophies

Patients from 76 independent families with various forms of mostly central retinal dystrophies were screened for mutations in the RDS/peripherin gene by means of SSCP analysis and direct DNA sequencing. Two nonsense mutations (Gln239ter, Tyr285ter), five missense mutations (Arg172Trp, Lys197Glu, Gly208Asp, Trp246Arg, Ser289Leu), and one single base insertion (Gly208insG), heterozygous in all cases, were detected. Only one of these mutations, Arg172Trp, has been reported previously. Cosegregation of the mutation with the disease phenotype could be established in selected families. Other missense mutations were excluded from a panel of 55-75 control subjects. The patients showed remarkable variation in phenotype and disease expression not only between cases with different mutations but also between affected members of the same family. This study indicates that RDS/peripherin mutations are a frequent cause of various types of central retinal dystrophies and that the RDS/peripherin gene exhibits a broad spectrum of allelic mutations. Comparative analysis of known mutations allowed us to hypothesise that the deleterious effect of RDS/peripherin gene mutations is the result of different molecular mechanisms.

Mutation analysis of the ND6 gene in patients with Lebers hereditary optic neuropathy

DNA sequence analysis of the gene encoding subunit 6 of the NADH-ubiquinone-oxidoreductase complex (ND6) in human mitochondria was performed in 25 independent patients who suffer from Lebers hereditary optic neuropathy (LHON). In 10 cases the well-known LHON mutation at nucleotide position (np) 14484 was detected. Furthermore, silent substitutions at np14167 and np14527 and missense mutations at np14498, np14564, np14568, and np14582 were found in individual patients. The np14498 and np14568 mutations were found in patients who present a typical clinical picture and course of LHON but lack any of the canonical mtDNA mutations. The np14568 mutation, which replaces a moderately conserved glycine by a serine residue, was observed in a single male patient and subsequently excluded in 175 independent controls. The mutation at np14498, which replaces an evolutionarily highly conserved tyrosine with a cysteine, was found in a multigeneration family with four affected members, the eldest carrying a heteroplasmic mixture of mutated and wildtype mtDNA molecules. None of 170 analyzed control subjects carried this mutation. These findings provide evidence that several allelic ND6 gene mutations may be involved in Lebers hereditary optic neuropathy.

Simultaneous detection of multiple point mutations using fluorescence-coupled competitive primer extension

We report the development of a method for the simultaneous genotyping of several distinct nucleotide positions by means of fluorescence-coupled competitive primer extension. We demonstrate the application of this method for the simultaneous detection of three point mutations in the human mitochondrial genome, at nucleotide positions 3460, 11778 and 14484, which account for about 90% of cases with Leber's hereditary optic neuropathy. mtDNA fragments encompassing these nucleotide positions are initially amplified in a multiplex PCR assay. Genotyping is then carried out by a simultaneous primer extension assay using wild-type-specific (FAM-labeled) and mutant-specific (JOE-labeled) oligonucleotides. Primer extension products are separated on a 6% polyacrylamide/8 M urea gel on a fluorescence DNA sequencer. Patients' genotypes can be derived from the peak color of the different-sized extension products. As little as 10% mutant DNA can be detected in heteroplasmic mixtures of wild-type and mutant mtDNA, a degree that is sufficient for routine clinical practice.

Analysis of 21 Stargardt's disease families confirms a major locus on chromosome 1p with evidence for non-allelic heterogeneity in a minority of cases

BACKGROUND

Autosomal recessive Stargardt's disease is a macular degeneration characterised by a juvenile onset and a rapidly progressive course resulting in an atrophic macular area typically surrounded by yellowish retinal flecks.

METHOD

The disease locus has previously been assigned to markers from chromosome 1p21-p13 by genetic linkage analysis in eight multiplex Stargardt's disease families.

RESULTS

In an extended analysis, the assignment to chromosome 1p was confirmed in the majority of the 21 families with Stargardt's disease who were studied. In addition, a series of recombinant chromosomes further narrowed the Stargardt's disease region to an approximately 3 cM interval between markers at D1S424 and D1S497.

CONCLUSION

Multipoint linkage analysis most probably excludes this locus in three of these families suggesting non-allelic heterogeneity with at least one additional minor Stargardt's disease locus.

Leber's hereditary optic neuropathy: clinical and molecular genetic results obtained in a family with a new point mutation at nucleotide position 14498 in the ND 6 gene

Mitochondrial DNA mutations at nucleotide position (np) 3460 in the ND 1 gene, np 11778 in the ND 4 gene, and np 14484 in the ND 6 gene are commonly considered to be associated with the clinical features of Leber's hereditary optic neuropathy (LHON) and account for the majority of LHON cases. Recently, a further mutation in the mtDNA at np 14459 was detected. Herein we report the clinical and the most relevant molecular genetic findings obtained in a LHON family with a new mitochondrial DNA mutations at np 14498 in the ND 6 gene. Clinical and historical data were collected over four generations on three affected and five yet unaffected relatives of the maternal line in this family. All three patients and four of their relatives underwent molecular genetic examination. Two patients and five relatives were also studied clinically. All patients exhibited typical clinical features of LHON. In all yet unaffected relatives, various degrees of peripapillary microangiopathy were found. Molecular analysis did not reveal any of the common LHON mutations. Sequence analysis of the mtDNA of one patient was performed and showed a thymine-to-cytosine exchange at np 14498 in the ND 6 gene, leading to the replacement of an evolutionary highly conserved tyrosine by a cysteine residue. The mutation was not found among 70 other LHON lineages and 180 controls. The new mutation at np 14498 lies in the vicinity of the LHON-related mutations at np 14484 and of the recently described mutation at np 14459, in a region constituting the most evolutionarily conserved part of this polypeptide. That the new mutation at np 14498 is found within this highly conserved region and was not present in any controls implies that this mutation is responsible for LHON in this family.

RNA editing of a group II intron in Oenothera as a prerequisite for splicing

The trans-splicing group II intron c/d in the Oenothera mitochondrial nad1 gene is modified by RNA editing in domain 6. This C-to-U conversion generates the typical domain 6 structure, which prompted us to speculate that this RNA editing event might be essential for splicing. To test this hypothesis, we investigated the influence of unedited and edited sequences of the Oenothera intron on splicing in vitro. The stem of domain 6 of intron nad1-c/d was transplanted into the autocatalytic yeast intron aI5c, yielding chimeras with the genomic C and the edited U, respectively, 5' of the branchpoint A. When incubated under self-splicing conditions, only the edited chimera was released as a lariat, while the precursor with the genomically coded C remained inactive. Our results support the hypothesis that Oenothera group II intron nad1-c/d cannot be spliced from the primary transcript without previous editing in domain 6.

[Correlation between clinical and molecular genetic findings in Leber's optic atrophy]

Leber's hereditary optic neuropathy (LHON) is associated with point mutations of mitochondrial DNA (mtDNA) that appear to be pathogenetic for this disease. These mutations affect nucleotide positions 3460, 4160, 11,778, 14,484, and possibly 15,257. The pathogenetic significance of other mtDNA point mutations (secondary mutations) is less clear. We reviewed the clinical and molecular genetic characteristics of 29 visually symptomatic patients from 26 families. In addition, we studied 54 relatives of the maternal line of these patients. Sixteen of them underwent clinical and molecular genetic examination; 38 underwent only molecular genetic examination. The 29 affected individuals showed a male predominance of 93.1% (27/29) and ages of onset of visual loss ranging from 15 to 55 years. The time interval between affected eyes was never longer than 1 year. Tobacco and/or alcohol abuse was common. Peripapillary microangiopathy was found in 20.7% (6/29) of our patients. The number of patients with peripapillary microangiopathy seems to be small, but we could not examine all patients early after onset of the disease: the time of first examination is critical for the diagnosis of peripapillary microangiopathy. From the 16 relatives who underwent clinical examination, 62.5% (10/16) also had peripapillary microangiopathy. Eighteen patients were analyzed by brain computed tomography or magnetic resonance imaging. Four definitely pathological results seem remarkably high in comparison with the results of other authors. Our LHON patients and their relatives invariably had an identical pattern of point mutations, both primary as well as secondary. Of the LHON patients, 79.3% had the primary mutation at position 11,778, 20.7% at position 3460. Different numbers and combinations of secondary mutations were observed in a large portion of both groups. Three patients with the 11,778 mutation noticed remarkable visual recovery. There was no clear correlation between the type and number of point mutations in the individual and the severity of the disease.

Differential RNA editing in closely related introns in Oenothera mitochondria

Introns a/b of the nad2 gene and b/c of the nad1 gene in Oenothera mitochondria were found to be closely related. Within a scaffold of conserved sequence regions, a 48 bp sequence element covering intron domain V and flanking nucleotides is identical in both group II introns. The third nucleotide of this element is edited in the nad2, but not in the nad1 intervening sequence. The C to U editing event compensates an nad2-specific nucleotide mismatch in the stem domain IV and thus improves secondary structure stability. This differential editing event indicates that the identical upstream 2 and downstream 45 nucleotides are not sufficient to specify this editing site. Comparison of adjacent exon editing patterns in spliced and unspliced transcripts shows a higher degree of editing in processed sequences, confirming that RNA editing is a posttranscriptional process in plant mitochondria.

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.

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.

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.

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.

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.

Duplicated Sequence Elements and Their Function in Plant Mitochondria

A considerable portion of the plant mitochondrial DNA is derived from genome internal duplications. Many of these amplified sequences determine functions of transcription and processing. Among these are promoter regions, sequences defining the 3′ ends of stable mRNAs, potential RNA processing sites and intron domains. Simultaneously, some of these repeated sequences can be active sites of recombination in plant mitochondria. Such duplicat­ed control regions may simplify coordinate expression of different genes.

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.

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.

Cytochrome oxidase subunit II mRNAs in Oenothera mitochondria are edited at 24 sites

Analysis of cDNA clones covering the entire coding region of cytochrome oxidase subunit II in Oenothera mitochondria reveals 24 potential editing sites: 23 C to U transitions and one U to C conversion. One editing event is observed outside the open reading frame in the 3' non-coding region. Thirteen editing sites are found altered in all cDNA clones, whereas the other eleven sites are only edited in some of the cDNA clones. These differentially edited sites occur most frequently at silent codon positions or in triplets at non-conserved amino acids.

RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition

RNA editing in the cytochrome b locus of Oenothera berteriana mitochondria modified a number of cytidine nucleotides to uridines, mostly altering codon identities. One nucleotide alteration involved a reverse modification changing a genomic thymidine to a cytidine in the cDNA sequence. The enzymatic editing activity in higher-plant mitochondria thus appears to be able to catalyze the interconversion of pyrimidines in both directions at specific nucleotides in the mRNA template.

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.

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.

RNA editing in plant mitochondria

Comparative sequence analysis of genomic and complementary DNA clones from several mitochondrial genes in the higher plant Oenothera revealed nucleotide sequence divergences between the genomic and the messenger RNA-derived sequences. These sequence alterations could be most easily explained by specific post-transcriptional nucleotide modifications. Most of the nucleotide exchanges in coding regions lead to altered codons in the mRNA that specify amino acids better conserved in evolution than those encoded by the genomic DNA. Several instances show that the genomic arginine codon CGG is edited in the mRNA to the tryptophan codon TGG in amino acid positions that are highly conserved as tryptophan in the homologous proteins of other species. This editing suggests that the standard genetic code is used in plant mitochondria and resolves the frequent coincidence of CGG codons and tryptophan in different plant species. The apparently frequent and non-species-specific equivalency of CGG and TGG codons in particular suggests that RNA editing is a common feature of all higher plant mitochondria.