Limits...
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Edgar AJ - BMC Genet. (2002)

Bottom Line: These truncated proteins are the result of 3 mutations within the gene.There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4.The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tissue Engineering & Regenerative Medicine Centre, Division of Investigative Science, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Chelsea & Westminster Hospital, London, United Kingdom. alasdair.edgar@ic.ac.uk

ABSTRACT

Background: L-threonine is an indispensable amino acid. One of the major L-threonine degradation pathways is the conversion of L-threonine via 2-amino-3-ketobutyrate to glycine. L-threonine dehydrogenase (EC 1.1.1.103) is the first enzyme in the pathway and catalyses the reaction: L-threonine + NAD+ = 2-amino-3-ketobutyrate + NADH. The murine and porcine L-threonine dehydrogenase genes (TDH) have been identified previously, but the human gene has not been identified.

Results: The human TDH gene is located at 8p23-22 and has 8 exons spanning 10 kb that would have been expected to encode a 369 residue ORF. However, 2 cDNA TDH transcripts encode truncated proteins of 157 and 230 residues. These truncated proteins are the result of 3 mutations within the gene. There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4. The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon. These truncated proteins would be non-functional since they have lost part of the NAD+ binding motif and the COOH terminal domain that is thought to be involved in binding L-threonine. TDH mRNA was present in all tissues examined.

Conclusions: The human L-threonine 3-dehydrogenase gene is an expressed pseudogene having lost the splice acceptor site preceding exon 6 and codon arginine-214 (CGA) is mutated to a stop codon (TGA).

Show MeSH
Comparison of the human TDH gene sequences in the region of exon 4 and 6 acceptor sites with those of other species. (A) The splice donor and acceptor sites are indicated (gt and ag respectively). There is a splice site mutation in exon 4 in one of the human genomic sequences (gg, coloured red). The translations of the genes are shown below the DNA sequences (ORF). The species and accession numbers are: Homo sapiens, HsTDH_gDNA_A (AF131216); HsTDH_gDNA_B (AC011959); Mus musculus, MmTDHgDNA (14.54000001-55000000 supercontig, Sanger Centre, UK) and puffer fish, Takifugu rubripes, TrTDH_gDNA (AF411956). (B) There is an in-frame stop codon (TGA, coloured blue) and a splice site mutation in exon 6 in the human genomic sequence (AF131216). A cryptic splice site (ag, coloured red) was utilised in cDNA clone 1 that altered the reading frame, resulting in another stop codon (TGA, coloured green). The species and accession numbers are: pig, Sus scrofa, SsTDH_cDNA (AY095535); MmTDH_cDNA (AY116662); rat, Rattus norvegicus, RmTDH_EST (BF557448); chicken, Gallus gallus, GgTDH_EST (BM491791); western clawed frog, Silurana tropicalis, StTDH_EST (AL638064); zebrafish, Danio rerio, DrTDH_ESTs; the tunicate, Ciona intestinalis, CiTDH_ESTs; fruit fly, Drosophila melanogaster, DmTDH_gDNA (AAF51607); the nematode, Caenorhabditis elegans, CeTDH_ESTs and the euglenoid, Trypanosoma brucei, TbTDH_gDNA (AC084047). There are no introns in this region of the fly, nematode and trypanosome genes (__). Identical nucleotides and residues are shown by *, strongly similar residues by: and weakly similar residues by (.).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC131051&req=5

Figure 5: Comparison of the human TDH gene sequences in the region of exon 4 and 6 acceptor sites with those of other species. (A) The splice donor and acceptor sites are indicated (gt and ag respectively). There is a splice site mutation in exon 4 in one of the human genomic sequences (gg, coloured red). The translations of the genes are shown below the DNA sequences (ORF). The species and accession numbers are: Homo sapiens, HsTDH_gDNA_A (AF131216); HsTDH_gDNA_B (AC011959); Mus musculus, MmTDHgDNA (14.54000001-55000000 supercontig, Sanger Centre, UK) and puffer fish, Takifugu rubripes, TrTDH_gDNA (AF411956). (B) There is an in-frame stop codon (TGA, coloured blue) and a splice site mutation in exon 6 in the human genomic sequence (AF131216). A cryptic splice site (ag, coloured red) was utilised in cDNA clone 1 that altered the reading frame, resulting in another stop codon (TGA, coloured green). The species and accession numbers are: pig, Sus scrofa, SsTDH_cDNA (AY095535); MmTDH_cDNA (AY116662); rat, Rattus norvegicus, RmTDH_EST (BF557448); chicken, Gallus gallus, GgTDH_EST (BM491791); western clawed frog, Silurana tropicalis, StTDH_EST (AL638064); zebrafish, Danio rerio, DrTDH_ESTs; the tunicate, Ciona intestinalis, CiTDH_ESTs; fruit fly, Drosophila melanogaster, DmTDH_gDNA (AAF51607); the nematode, Caenorhabditis elegans, CeTDH_ESTs and the euglenoid, Trypanosoma brucei, TbTDH_gDNA (AC084047). There are no introns in this region of the fly, nematode and trypanosome genes (__). Identical nucleotides and residues are shown by *, strongly similar residues by: and weakly similar residues by (.).

Mentions: To determine whether these mutations were present in other species, sequence alignments around the acceptor splice sites in exons 4 and 6 were constructed (Fig. 5). The genomic sequences from the mouse and puffer fish (Takifugu rubripes or Fugu) and another human genomic clone (AF131216, Institute of Molecular Biotechnology, Germany) have intact acceptor splice sites in exon 4 suggesting that the loss of this splice site is a single nucleotide polymorphism (SNP) (Fig. 5A). In both human genomic DNA sequences the acceptor splice site in exon 6 is lost, but it is intact in both the mouse and puffer fish sequences (Fig. 5B). Similarly, the stop codon is present in both human genomic DNA sequences, but it is not present in genomic DNA, cDNA and EST sequences from other species. In human genomic DNA sequence (AC011959) there is also an A to T mutation in codon 201 (ATG to TTG, in exon 5) resulting a methionine to leucine substitution.


The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Edgar AJ - BMC Genet. (2002)

Comparison of the human TDH gene sequences in the region of exon 4 and 6 acceptor sites with those of other species. (A) The splice donor and acceptor sites are indicated (gt and ag respectively). There is a splice site mutation in exon 4 in one of the human genomic sequences (gg, coloured red). The translations of the genes are shown below the DNA sequences (ORF). The species and accession numbers are: Homo sapiens, HsTDH_gDNA_A (AF131216); HsTDH_gDNA_B (AC011959); Mus musculus, MmTDHgDNA (14.54000001-55000000 supercontig, Sanger Centre, UK) and puffer fish, Takifugu rubripes, TrTDH_gDNA (AF411956). (B) There is an in-frame stop codon (TGA, coloured blue) and a splice site mutation in exon 6 in the human genomic sequence (AF131216). A cryptic splice site (ag, coloured red) was utilised in cDNA clone 1 that altered the reading frame, resulting in another stop codon (TGA, coloured green). The species and accession numbers are: pig, Sus scrofa, SsTDH_cDNA (AY095535); MmTDH_cDNA (AY116662); rat, Rattus norvegicus, RmTDH_EST (BF557448); chicken, Gallus gallus, GgTDH_EST (BM491791); western clawed frog, Silurana tropicalis, StTDH_EST (AL638064); zebrafish, Danio rerio, DrTDH_ESTs; the tunicate, Ciona intestinalis, CiTDH_ESTs; fruit fly, Drosophila melanogaster, DmTDH_gDNA (AAF51607); the nematode, Caenorhabditis elegans, CeTDH_ESTs and the euglenoid, Trypanosoma brucei, TbTDH_gDNA (AC084047). There are no introns in this region of the fly, nematode and trypanosome genes (__). Identical nucleotides and residues are shown by *, strongly similar residues by: and weakly similar residues by (.).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC131051&req=5

Figure 5: Comparison of the human TDH gene sequences in the region of exon 4 and 6 acceptor sites with those of other species. (A) The splice donor and acceptor sites are indicated (gt and ag respectively). There is a splice site mutation in exon 4 in one of the human genomic sequences (gg, coloured red). The translations of the genes are shown below the DNA sequences (ORF). The species and accession numbers are: Homo sapiens, HsTDH_gDNA_A (AF131216); HsTDH_gDNA_B (AC011959); Mus musculus, MmTDHgDNA (14.54000001-55000000 supercontig, Sanger Centre, UK) and puffer fish, Takifugu rubripes, TrTDH_gDNA (AF411956). (B) There is an in-frame stop codon (TGA, coloured blue) and a splice site mutation in exon 6 in the human genomic sequence (AF131216). A cryptic splice site (ag, coloured red) was utilised in cDNA clone 1 that altered the reading frame, resulting in another stop codon (TGA, coloured green). The species and accession numbers are: pig, Sus scrofa, SsTDH_cDNA (AY095535); MmTDH_cDNA (AY116662); rat, Rattus norvegicus, RmTDH_EST (BF557448); chicken, Gallus gallus, GgTDH_EST (BM491791); western clawed frog, Silurana tropicalis, StTDH_EST (AL638064); zebrafish, Danio rerio, DrTDH_ESTs; the tunicate, Ciona intestinalis, CiTDH_ESTs; fruit fly, Drosophila melanogaster, DmTDH_gDNA (AAF51607); the nematode, Caenorhabditis elegans, CeTDH_ESTs and the euglenoid, Trypanosoma brucei, TbTDH_gDNA (AC084047). There are no introns in this region of the fly, nematode and trypanosome genes (__). Identical nucleotides and residues are shown by *, strongly similar residues by: and weakly similar residues by (.).
Mentions: To determine whether these mutations were present in other species, sequence alignments around the acceptor splice sites in exons 4 and 6 were constructed (Fig. 5). The genomic sequences from the mouse and puffer fish (Takifugu rubripes or Fugu) and another human genomic clone (AF131216, Institute of Molecular Biotechnology, Germany) have intact acceptor splice sites in exon 4 suggesting that the loss of this splice site is a single nucleotide polymorphism (SNP) (Fig. 5A). In both human genomic DNA sequences the acceptor splice site in exon 6 is lost, but it is intact in both the mouse and puffer fish sequences (Fig. 5B). Similarly, the stop codon is present in both human genomic DNA sequences, but it is not present in genomic DNA, cDNA and EST sequences from other species. In human genomic DNA sequence (AC011959) there is also an A to T mutation in codon 201 (ATG to TTG, in exon 5) resulting a methionine to leucine substitution.

Bottom Line: These truncated proteins are the result of 3 mutations within the gene.There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4.The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon.

View Article: PubMed Central - HTML - PubMed

Affiliation: Tissue Engineering & Regenerative Medicine Centre, Division of Investigative Science, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Chelsea & Westminster Hospital, London, United Kingdom. alasdair.edgar@ic.ac.uk

ABSTRACT

Background: L-threonine is an indispensable amino acid. One of the major L-threonine degradation pathways is the conversion of L-threonine via 2-amino-3-ketobutyrate to glycine. L-threonine dehydrogenase (EC 1.1.1.103) is the first enzyme in the pathway and catalyses the reaction: L-threonine + NAD+ = 2-amino-3-ketobutyrate + NADH. The murine and porcine L-threonine dehydrogenase genes (TDH) have been identified previously, but the human gene has not been identified.

Results: The human TDH gene is located at 8p23-22 and has 8 exons spanning 10 kb that would have been expected to encode a 369 residue ORF. However, 2 cDNA TDH transcripts encode truncated proteins of 157 and 230 residues. These truncated proteins are the result of 3 mutations within the gene. There is a SNP, A to G, present in the genomic DNA sequence of some individuals which results in the loss of the acceptor splice site preceding exon 4. The acceptor splice site preceding exon 6 was lost in all 23 individuals genotyped and there is an in-frame stop codon in exon 6 (CGA to TGA) resulting in arginine-214 being replaced by a stop codon. These truncated proteins would be non-functional since they have lost part of the NAD+ binding motif and the COOH terminal domain that is thought to be involved in binding L-threonine. TDH mRNA was present in all tissues examined.

Conclusions: The human L-threonine 3-dehydrogenase gene is an expressed pseudogene having lost the splice acceptor site preceding exon 6 and codon arginine-214 (CGA) is mutated to a stop codon (TGA).

Show MeSH