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BMC Genetics Biomed Central CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central BMC Genetics BioMed Central Research3 BMC2002, Genetics article x Open Access The human L-threonine 3-dehydrogenase gene is an expressed pseudogene Alasdair J Edgar Address: 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 E-mail: [email protected] Published: 2 October 2002 Received: 29 July 2002 Accepted: 2 October 2002 BMC Genetics 2002, 3:18 This article is available from: http://www.biomedcentral.com/1471-2156/3/18 © 2002 Edgar; licensee BioMed Central Ltd. This article is published in Open Access: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. 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). Background ducts new drug metabolism and pharmacokinetic studies Liver failure is a cause of considerable mortality; therefore on key mammal species [4]. bioartificial livers may offer significant therapeutic bene- fit. Porcine-derived hepatocytes are being used in clinical The liver plays a critical role in regulating the circulating studies of bioartificial livers [1,2]. There may, however, be concentrations of amino acids. The regulation of amino significant differences in the activities of liver enzymes be- acid supply to bioartificial organs and maintaining the ac- tween species [3]. These differences are also important tivity of the amino acid-metabolising enzymes will be im- considerations when the pharmaceutical industry con- portant in their development. Active maintenance of the Page 1 of 13 (page number not for citation purposes) BMC Genetics 2002, 3 http://www.biomedcentral.com/1471-2156/3/18 optimal amino acid concentrations will offer the possibil- duction of labelled glycine and CO2 in adults and suggest- ity of prolonging the differentiated function of hepato- ed that there was some threonine catabolism via the cytes in bioartificial livers [5]. threonine dehydrogenase pathway, but it accounted for only 7–11% of total [21]. This suggested that the L-serine/ L-threonine is one of three indispensable amino acids threonine dehydratase pathway is the dominant route in since mammals do not possess the necessary enzymes for the catabolism of threonine in humans. the transamination of threonine [6]. However, the tran- sient apoenzyme form of L-threonine dehydratase bound Recently, the sequences of the murine and porcine TDH to pyridoxamine 5'-phosphate dehydratase can carry out a cDNAs have been reported [22]. The amino-terminal re- half-transamination of L-threonine [7]. Once L-threonine gions of these proteins have characteristics of a mitochon- is oxidised through various catabolic pathways it is lost for drial targeting sequence and are related to the UDP- the purposes of protein synthesis. Therefore, it is impor- galactose 4-epimerases, with both enzyme families having tant for determining levels of human nutrition that factors an amino-terminal NAD+ binding domain. The sequence regulating threonine oxidation are identified. The interna- of the human KBL transcript, the second enzyme in the tional recommended intake of L-threonine for adults is 7 pathway, has also been described [23] and this study mg.kg-1.d-1[8]. However, this has recently been chal- aimed to identify the human TDH gene. lenged as being too low and a recommendation of 15 mg.kg-1.d-1 has been suggested [9]. Results Human TDH gene There are two major L-threonine degradation pathways. L- The murine L-threonine 3-dehydrogenase gene (TDH) has threonine is either catabolised by L-threonine 3-dehydro- recently been identified [22]. The human genome was genase to 2-amino-3-ketobutyrate or by L-serine/threo- searched using this murine sequence and only a single pu- + nine dehydratase (EC 4.2.1.16) to NH4 and 2- tative human TDH gene was found to be present. The pu- ketobutyrate. In both eukaryotic and prokaryotic cells, the tative human TDH gene is located on clone RP11-110L10, conversion of L-threonine via 2-amino-3-ketobutyrate to chromosome 8p23-22 (GenBank accession No. glycine takes place in a two-step process [10,11]. L-threo- AC011959, Whitehead Institute/MIT Center for Genome nine dehydrogenase catalyses the reaction: L-threonine + Research, USA), between the gene for acyl-malonyl con- NAD+ = 2-amino-3-ketobutyrate + NADH. The subse- densing enzyme and hypothetical protein, C8orf13 gene quent reaction between 2-amino-3-ketobutyrate and (accession No. XP_088377) (Figure 1A). By comparison coenzyme A to form glycine and acetyl-CoA is catalysed by with the murine TDH gene and the porcine cDNA, 8 hu- 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29 man exons were identified spanning 10 kb (Figure 1B). also called glycine acetyltransferase; gene names KBL and The predicted start of the ORF is in good sequence context GCAT). L-threonine dehydrogenase and 2-amino-3-keto- for the initiation of translation [24]. butyrate coenzyme A ligase are associated physically on the inner membrane-matrix of mitochondria where the The sequence of the human TDH exons (Fig. 2) has 84% two enzymes form a complex with a stoichiometry of one identity with the porcine cDNA at the nucleotide level in threonine dehydrogenase tetramer to two 2-amino-3-ke- the ORF and the theoretical full-length human protein has tobutyrate coenzyme A ligase dimers [12–14]. 85% identity and 97% similarity with the porcine TDH protein [22], suggesting that this is the human TDH gene. In mammals, the removal of the 1-carbon of threonine is The first potential polyadenylation signal site (ATTAAA) is thought to occur through threonine dehydrogenase, this also conserved between species. carbon being incorporated into glycine and released as CO2 by the mitochondrial glycine cleavage system. In nor- Human TDH protein mally-fed pigs and rats 80 to 87% of L-threonine catabo- The predicted human TDH protein possesses very weak lism occurs via threonine dehydrogenase [15,16] and in similarity to the human uridine diphosphogalactose-4- isolated rat and cat hepatocytes 35% to 50% of threonine epimerase protein (GALE). GALE catalyses the intercon- oxidation occurs through this pathway [17,18]. Zhao et al. version of UDP-galactose and UDP-glucose in the meta- measured threonine oxidation in adult humans by the bolic pathway that converts galactose into glucose1- 13 production of labelled CO2 from L-[1- C]threonine and phosphate, and also catalyses the interconversion of UDP- concluded that the conversion of threonine to glycine GalNAc and UDP-GlcNAc. An alignment of the human through the threonine dehydrogenase pathway was not TDH protein with other eukaryotic TDH protein sequenc- important if it exists at all [19]. However, the dehydroge- es and GALE proteins from Homo sapiens and Escherichia nase pathway is thought to account for 44% of total thre- coli identified conserved residues likely to contact the onine oxidation in infants [20]. More recently, the same nicotinamide-adenine-dinucleotide cofactor (NAD+) group used a more sensitive method to measure the pro- (Fig. 3) [25]. They are Gly-58, Gly-61, Gly-64, Asp-84, Page 2 of 13 (page number not for citation purposes) BMC Genetics 2002, 3 http://www.biomedcentral.com/1471-2156/3/18 A 8p23 MTMR8 AMAC TDH C8orf13 BLK 8p22 Tel Cen B 34 176 kb 1kb AAGAAAATGC TGA ATTAAA Exon 1 2 3 4 5 6 7 8 172 43 71 150 173 91 270 137/369 Intron 1844 1235 2102 99 1075 1744 593 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 dehydro- genase, 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.
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