Exon mapping by PCR

Succinyl-CoA:3-ketoacid CoA transferase (SCOT): cloning of the human SCOT gene, tertiary structural modeling of the human SCOT monomer, and characterization of three pathogenic mutations

The activity of succinyl-CoA:3-ketoacid CoA transferase (SCOT; locus symbol OXCT; EC 2.8.3.5) is the main determinant of the ketolytic capacity of tissues. Hereditary SCOT deficiency causes episodic ketoacidosis. Here we describe the human SCOT gene, which spans more than 100 kb and contains 17 exons, on chromosome 5p13. We report pathogenic missense mutations in three SCOT-deficient patients designated GS04, 05, and 06. GS04 is a G219E/G324E compound; GS05 is a V221M homozygote, and GS06 is a G324E homozygote. We constructed a tertiary structural model of human SCOT by homology modeling based on the known structure of Acidaminococcus fermentans glutaconate CoA transferase. The model predicts that V221 and G219 are on the dimerizing surface, whereas G324 is near the active site. SCOT activity was reduced to a comparable degree in all three patients, but in a transient expression assay in SCOT-deficient fibroblasts, cDNAs containing G219E and G324E produced no detectable activity, whereas V221M constructs yielded approximately 10% of the control peptide level and detectable specific activity. Interestingly, GS05 had the mildest clinical course reported to date and detectable levels of SCOT protein in fibroblasts.

Characterization of the mouse Rep-3 gene: sequence similarities to bacterial and yeast mismatch-repair proteins

The mouse Rep-3 gene is transcribed divergently from the same promoter region as the dihydrofolate reductase-encoding gene and has a deduced amino-acid sequence that shares identity with the bacterial protein, MutS, which is involved in DNA mismatch repair. We have cloned Rep-3, mapped it and sequenced all of the known exons and their intron junction sequences. We find that the open reading frame is considerably larger than initially reported and that the most abundant form of Rep-3 mRNA encodes a protein of 123 kDa. The gene spans at least 134 kb and consists of 26 exons, including several alternatively spliced exons. All of the exon/intron junctions match the expected consensus sequences with the exception of the splice junctions for intron 6, which has AT and AC dinucleotides instead of the usual GT and AG bordering the exon sequences. The junction sequences for this intron share consensus sequences with three intron sequences from other genes, thereby helping to establish an alternative consensus sequence.