Identification of ‘Amigo’ and ‘Kavkaz’ translocations in Ohio soft red winter wheats (Triticum aestivum L.)

One cultivar (GR876) and two advanced Ohio soft red winter wheat lines (OH413 and OH414), with Kavkaz in their pedigrees, were examined for the presence of the Kavkaz, 1RS/1BL rye/wheat chromosome translocation. Another advanced line (OH416), with Amigo in its pedigree, was examined for the presence of the Amigo, 1RS/1AL translocation. Only two satellited chromosomes were observed in most mitotic root-tip cells from GR876, OH413, and OH414, compared to four in most cells from OH416. Heteromorphic bivalents were observed in most PMCs from hybrids produced by crossing GR876, OH413, and OH414 as females to Chinese Spring. No heteromorphic bivalents were observed in PMCs from OH416 x Chinese Spring hybrids. When GR876 and the Ohio lines were hybridized with Chinese Spring dimonotelosomic-1B, telosomic trivalents, consisting of the short- and longarm telosomes paired with chromosome 1B, were only observed in PMCs from 43-chromosome hybrids involving OH416. The long-arm telosome paired with the translocation chromosome, while the short-arm telosome remained unpaired in all other 43-chromosome hybrids. Separation of gliadin proteins from GR876 and the Ohio lines by PAGE revealed that secalin bands for GR876, OH413, and OH414, migrated similarly to the secalins for Kavkaz. Bands for OH416, identified as possible secalins, migrated similarly to those for Amigo. Cultivar GR876 and advanced Ohio soft red winter wheat lines OH413 and OH414 carry the Kavkaz translocation, while OH416 carries the Amigo translocation.Communicated by K. Tsunewaki     

The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: Causes and consequences

Summary A total of 101 different examples of point mutations, which lie in the vicinity of mRNA splice junctions, and which have been held to be responsible for a human genetic disease by altering the accuracy of efficiency of mRNA splicing, have been collated. These data comprise 62 mutations at 5 splice sites, 26 at 3 splice sites and 13 that result in the creation of novel splice sites. It is estimated that up to 15% of all point mutations causing human genetic disease result in an mRNA splicing defect. Of the 5 splice site mutations, 60% involved the invariant GT dinucleotide; mutations were found to be non-randomly distributed with an excess over expectation at positions +1 and +2, and apparent deficiencies at positions –1 and –2. Of the 3 splice site mutations, 87% involved the invariant AG dinucleotide; an excess of mutations over expectation was noted at position -2. This non-randomness of mutation reflects the evolutionary conservation apparent in splice site consensus sequences drawn up previously from primate genes, and is most probably attributable to detection bias resulting from the differing phenotypic severity of specific lesions. The spectrum of point mutations was also drastically skewed: purines were significantly overrepresented as substituting nucleotides, perhaps because of steric hindrance (e.g. in U1 snRNA binding at 5 splice sites). Furthermore, splice sites affected by point mutations resulting in human genetic disease were markedly different from the splice site consensus sequences. When similarity was quantified by a consensus value, both extremely low and extremely high values were notably absent from the wild-type sequences of the mutated splice sites. Splice sites of intermediate similarity to the consensus sequence may thus be more prone to the deleterious effects of mutation. Regarding the phenotypic effects of mutations on mRNA splicing, exon skipping occurred more frequently than cryptic splice site usage. Evidence is presented that indicates that, at least for 5 splice site mutations, cryptic splice site usage is favoured under conditions where (1) a number of such sites are present in the immediate vicinity and (2) these sites exhibit sufficient homology to the splice site consensus sequence for them to be able to compete successfully with the mutated splice site. The novel concept of a potential for cryptic splice site usage value was introduced in order to quantify these characteristics, and to predict the relative proportion of exon skipping vs cryptic splice site utilization consequent to the introduction of a mutation at a normal splice site.     

An isolated β 1 exon next to the DR α gene in the HLA-D region

A cosmid clone containing the DR gene and a ₁ exon of a DR -related gene was isolated from a human cosmid clone bank made from the consanguineous DR7 cell line MANN. No other DR-related exons were found on this clone. The ₁ exon was located about 15 kb away from the DR gene in a tail-to-tail (3 to 3) orientation. The exon contained several deleterious mutations: a defective splice site at the 5 end, two translational frame shifts (a 1 by deletion and a 1 bp insertion), and three extra cysteine residues. Nucleotide and amino acid sequence comparisons of the ₁ exon indicated that although it is substantially different from other class II -chain genes, it is slightly more related to DR than to any other class 11 gene. The DR-related sequence was on a DNA fragment which showed no polymorphism on a panel of cell lines with Eco RI or Pst 1. These Southern blots, however, revealed a related, polymorphic sequence in the human genome. Nucleotide sequences in the intron flanking the ₁ exon shared greater sequence homology than the ₁ exon itself when compared with the DR genomic sequence. The exon may play a role in the generation of variation in expressed class II -chain genes and it may be a relic of a different subset of class II products.     

Tyrosinemia type 1 — complex splicing defects and a missense mutation in the fumarylacetoacetase gene

Two mutations are reported in six tyrosinemia type 1 patients from northern Europe. In four patients, a G to A transition at nucleotide position 1009 (G¹⁰⁰⁹A) of the fumarylacetoacetase (FAH) coding sequence caused aberrant splicing by introducing an acceptor splice site within exon 12, thereby deleting the first 50 nucleotides of this exon. The following exon-intron boundary was frequently missed, and a cryptic donor splice site within intron 12 caused a partial intron 12 retention of 105 bp. This point mutation alternatively gave a glycine 337 to serine substitution in instances of correct splicing. The mutation is rapidly detected by PvuII digestion of polymerase chain reaction (PCR)-amplified genomic DNA. Another mutation, g⁺⁵a in the intron 12 donor splice site consensus sequence (IVS12 g⁺⁵a), was found in five of the patients. This caused alternative splicing with retention of the first 105 nucleotides of intron 12, exon 12 skipping, and a combined deletion of exons 12 and 13. Rapid detection of this mutation is achieved by restriction digestion of PCR-amplified genomic DNA; a mismatch primer combined with the point mutation creates a Tru9I restriction site. One patient who was homozygous for the G¹⁰⁰⁹A mutation had a chronic form of tyrosinemia. Three patients were combined heterozygotes for G¹⁰⁰⁹A and TVS12 g⁺⁵a. Their clinical phenotypes varied from acute to chronic, indicating the impact of background genes and/or external factors on the presentation of typrosinemia type 1.     

Characterization and transcript analysis of the major phycobiliprotein subunit genes from Aglaothamnion neglectum (Rhodophyta)

The genes encoding the and subunits of allophycocyanin, phycocyanin and phycoerythrin from the red alga Aglaothamnion neglectum were isolated and characterized. While the operons containing the different phycobiliprotein genes are dispersed on the plastid genome, the genes encoding the and subunits for each phycobiliprotein are contiguous. The subunit gene is 5 for both the phycocyanin and phycoerythrin operons, while the subunit gene is 5 for the allophycocyanin operon. The amino acid sequences of A. neglectum phycobiliproteins, as deduced from the nucleotide sequences of the genes, are 65–85% identical to analogous proteins from other red algae and cyanobacteria. The conserved nature of the plastid-encoded red algal and cyanobacterial phycobiliprotein genes supports the proposed origin of red algal plastids from cyanobacterial endosymbionts.Many environmental factors effect phycobilisome biosynthesis. The effect of both nutrient availability and light quantity on the level of A. neglectum phycobiliprotein subunits and the mRNA species encoding those subunits is described.     

Arabidopsis consensus intron sequences

We have analysed 998 Arabidopsis intron sequences in the EMBL database. All Arabidopsis introns to adhere to the :GU...AG: rule with the exception of 1% of introns with :GC at their 5 ends. Virtually all of the introns contained a putative branchpoint sequence (YUNAN) 18 to 60 nt upstream of the 3 splice site. Although a polypyrimidine tract was much less apparent than in vertebrate introns, the most common nucleotide in the region upstream of the 3 splice site was uridine. Consensus sequences for 5 and 3 splice sites and branchpoint sequences for Arabidopsis introns are presented.     

Exon shuffling in anther-specific genes from sunflower

We describe here the nucleotide sequence of an anther-specific gene (sf18) from sunflower, encoding a proline- and glycine-rich polypeptide with a hydrophobic amino-terminus (signal peptide). The gene is split by a 211 by intron and is partially related to another anther-specific gene (sf2) from sunflower with which it shares important sequence stretches in the 5 coding and upstream regions. We propose that the two genes have originated via exon shuffling, during which a copy of a DNA segment including the promoter region as well as a signal peptide coding sequence has been transferred into the upstream region of two different potential coding sequences, generating two novel genes which display the same specificity of expression and which both encode an extracellular protein. While the 5 region of the intron is highly conserved as part of the transferred region and may play a role in the selection of the 5 splice site, a common octanucleotide at the 3 end of the intron of the two genes might be involved in 3 splice site selection.