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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.

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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).

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Chromosomal localisation and gene structure of the human TDH gene. (A) The human TDH gene is located at 8p23 and the neighbouring genes are: myotubularin related protein 8, MTMR8: acyl-malonyl condensing enzyme, AMAC: threonine dehydrogenase, TDH: hypothetical protein, C8orf13; B lymphoid tyrosine kinase, BLK. Genes encoded by + and - stands are shown above and below the line respectively. The telomeric and centromeric directions are indicated. (B) The human TDH gene spans 10 kb and consists of 8 exons. The putative initiation methionine codon, stop codon and poly-adenylation signal are shown. Closed boxes indicate the ORF and the sizes (in bp) of the exons and introns are indicated.
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Figure 1: Chromosomal localisation and gene structure of the human TDH gene. (A) The human TDH gene is located at 8p23 and the neighbouring genes are: myotubularin related protein 8, MTMR8: acyl-malonyl condensing enzyme, AMAC: threonine dehydrogenase, TDH: hypothetical protein, C8orf13; B lymphoid tyrosine kinase, BLK. Genes encoded by + and - stands are shown above and below the line respectively. The telomeric and centromeric directions are indicated. (B) The human TDH gene spans 10 kb and consists of 8 exons. The putative initiation methionine codon, stop codon and poly-adenylation signal are shown. Closed boxes indicate the ORF and the sizes (in bp) of the exons and introns are indicated.

Mentions: The murine L-threonine 3-dehydrogenase gene (TDH) has recently been identified [22]. The human genome was searched using this murine sequence and only a single putative human TDH gene was found to be present. The putative human TDH gene is located on clone RP11-110L10, chromosome 8p23-22 (GenBank accession No. AC011959, Whitehead Institute/MIT Center for Genome Research, USA), between the gene for acyl-malonyl condensing enzyme and hypothetical protein, C8orf13 gene (accession No. XP_088377) (Figure 1A). By comparison with the murine TDH gene and the porcine cDNA, 8 human exons were identified spanning 10 kb (Figure 1B). The predicted start of the ORF is in good sequence context for the initiation of translation [24].


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

Edgar AJ - BMC Genet. (2002)

Chromosomal localisation and gene structure of the human TDH gene. (A) The human TDH gene is located at 8p23 and the neighbouring genes are: myotubularin related protein 8, MTMR8: acyl-malonyl condensing enzyme, AMAC: threonine dehydrogenase, TDH: hypothetical protein, C8orf13; B lymphoid tyrosine kinase, BLK. Genes encoded by + and - stands are shown above and below the line respectively. The telomeric and centromeric directions are indicated. (B) The human TDH gene spans 10 kb and consists of 8 exons. The putative initiation methionine codon, stop codon and poly-adenylation signal are shown. Closed boxes indicate the ORF and the sizes (in bp) of the exons and introns are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Chromosomal localisation and gene structure of the human TDH gene. (A) The human TDH gene is located at 8p23 and the neighbouring genes are: myotubularin related protein 8, MTMR8: acyl-malonyl condensing enzyme, AMAC: threonine dehydrogenase, TDH: hypothetical protein, C8orf13; B lymphoid tyrosine kinase, BLK. Genes encoded by + and - stands are shown above and below the line respectively. The telomeric and centromeric directions are indicated. (B) The human TDH gene spans 10 kb and consists of 8 exons. The putative initiation methionine codon, stop codon and poly-adenylation signal are shown. Closed boxes indicate the ORF and the sizes (in bp) of the exons and introns are indicated.
Mentions: The murine L-threonine 3-dehydrogenase gene (TDH) has recently been identified [22]. The human genome was searched using this murine sequence and only a single putative human TDH gene was found to be present. The putative human TDH gene is located on clone RP11-110L10, chromosome 8p23-22 (GenBank accession No. AC011959, Whitehead Institute/MIT Center for Genome Research, USA), between the gene for acyl-malonyl condensing enzyme and hypothetical protein, C8orf13 gene (accession No. XP_088377) (Figure 1A). By comparison with the murine TDH gene and the porcine cDNA, 8 human exons were identified spanning 10 kb (Figure 1B). The predicted start of the ORF is in good sequence context for the initiation of translation [24].

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