Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene
© Edgar; licensee BioMed Central Ltd. 2005
Received: 24 December 2004
Accepted: 09 March 2005
Published: 09 March 2005
There are three pathways of L-threonine catabolism. The enzyme L-threonine aldolase (TA) has been shown to catalyse the conversion of L-threonine to yield glycine and acetaldehyde in bacteria, fungi and plants. Low levels of TA enzymatic activity have been found in vertebrates. It has been suggested that any detectable activity is due to serine hydroxymethyltransferase and that mammals lack a genuine threonine aldolase.
The 7-exon murine L-threonine aldolase gene (GLY1) is located on chromosome 11, spanning 5.6 kb. The cDNA encodes a 400-residue protein. The protein has 81% similarity with the bacterium Thermotoga maritima TA. Almost all known functional residues are conserved between the two proteins including Lys242 that forms a Schiff-base with the cofactor, pyridoxal-5'-phosphate. The human TA gene is located at 17q25. It contains two single nucleotide deletions, in exons 4 and 7, which cause frame-shifts and a premature in-frame stop codon towards the carboxy-terminal. Expression of human TA mRNA was undetectable by RT-PCR. In mice, TA mRNA was found at low levels in a range of adult tissues, being highest in prostate, heart and liver. In contrast, serine/threonine dehydratase, another enzyme that catabolises L-threonine, is expressed very highly only in the liver. Serine dehydratase-like 1, also was most abundant in the liver. In whole mouse embryos TA mRNA expression was low prior to E-15 increasing more than four-fold by E-17.
Mice, the western-clawed frog and the zebrafish have transcribed threonine aldolase/GLY1 genes, but the human homolog is a non-transcribed pseudogene. Serine dehydratase-like 1 is a putative L-threonine catabolising enzyme.
Elucidating the factors involved in threonine homoeostasis is important for the development of nutritional strategies in human clinical diets for treating patients suffering from wasting diseases. In farmed animals the regulation of livestock feed is required to ensure optimal growth and to reduce nitrogen excretion which poses environmental disposal problems. Threonine is required for protein synthesis and the removal of excess threonine by oxidation is needed to prevent its accumulation both intracellularly and in the circulation. The rate of catabolism of many amino acids, including threonine, increases when dietary protein exceeds the body's requirements. Gluconeogenesis occurs mainly in the liver where it helps maintain blood glucose homeostasis in mammals. During starvation amino acid catabolism increases to support gluconeogenesis. Glucocorticoids and glucagon hormones are known to up regulate and insulin down regulate the gene expression of many amino acid-catabolising enzymes .
There are three L-threonine (L-alpha-amino-beta-hydroxybutyric acid) degradation pathways in living organisms; via L-threonine aldolase (L-TA)(EC 18.104.22.168)(gene abbreviation GLY1), via L-serine/threonine dehydratase (SDH)(EC 22.214.171.124)(gene abbreviation SDS)(in bacteria also called L-threonine deaminase) and via L-threonine 3-dehydrogenase (EC 126.96.36.199)(TDH) [2–5]. L-threonine is broken down by; L-TA to yield glycine and acetaldehyde, by SDH to yield NH4+ and 2-ketobutyrate and TDH to yield 2-amino-3-ketobutyrate. The subsequent reaction between 2-amino-3-ketobutyrate and coenzyme A to form glycine and acetyl-CoA is catalysed by 2-amino-3-ketobutyrate coenzyme A ligase (KBL)(EC 188.8.131.52), also called glycine acetyltransferase (gene abbreviation GCAT).
Together with the cofactor, pyridoxal-5'-phosphate (PLP), SDH uses threonine and serine as substrates to generate glycine which is used in gluconeogenesis. Serine dehydratase-like 1 gene (SDH1) is a second SDH gene found in vertebrates, but has yet to be characterised. I suggest that it is also a putative L-threonine catabolising enzyme.
Vitamin B6-dependant enzymes can be grouped according to their fold type. L-TA belongs to fold type I. L-TA enzymes are unrelated to D-TA enzymes which possess type III folds . In vertebrates, the TA enzyme has not been purified by protein fractionation, only assayed in homogenised tissue fractions and isolated hepatocytes. In vertebrates most L-threonine degradation occurs via the enzymatic activities of serine/threonine dehydratase and threonine dehydrogenase. However, the presence of threonine aldolase enzymatic activity has been demonstrate in rat liver extracts [7–14]. Threonine aldolase contributes 1–3% of total threonine degradation under a variety of nutritional states in both rat and quail [4, 15].
L-TAs from a number of species of bacteria and fungi have been isolated and characterized (reviewed in ). In the yeast, Saccharomyces cerevisiae, the glycine synthase-1 gene, GLY1 was identified as threonine aldolase [17, 18]. Previously, gene ablation studies had shown that the GLY1 pathway is a major source of glycine . But it only plays a minor role in Candida albicans . In a number of bacteria species such as Escherichia coli, Aeromonas jandaei, Pseudomonas and Thermatoga maritima the GLY1 gene has been cloned and their enzymatic activity characterised [21–24]. In thale cress, Arabidopsis thaliana, there are two threonine aldolase genes (THA1 and THA2). THA1 has been shown to play a role in seed nutritional quality . Putative GLY1 genes have been also identified in nematodes and flies . Recently, the X-ray crystal structures of L-threonine aldolase from the bacteria Thermotoga maritima have been determined as the apo-enzyme, bound to L-allo-threonine and to glycine .
These GLY1/threonine aldolases are distinct from the serine hydroxymethyltransferases (EC 184.108.40.206)(SHMT). However, some SHMT also possess some threonine aldolase enzymatic activity. SHMT from E. coli and the yogurt bacterium, Streptococcus thermophilus, have TA activity [26, 27]. SHMT isolated from rabbit liver has been shown to possess weak TA activity . Consequently, it has been thought that the minor threonine aldolase activity in liver extracts was due solely to SHMT, and that mammals lack a true threonine aldolase, but this has been questioned . Here I report that TA genes are present in vertebrates.
Analysis of murine L-threonine aldolase cdnas
Predicted secondary structure of the murine threonine aldolase protein
Sequence homology to other vertebrate threonine aldolase proteins
Human GLY1/threonine aldolase gene is a pseudogene
A database search identified 17q25 as the location for the human GLY1 gene. All exon/intron boundaries found in the murine threonine aldolase gene are conserved in man. The mouse to human conserved synteny map shows that both GLY1 genes have the synaptogyrin 2 (SYNGR2), baculoviral IAP repeat-containing 5 (BIRC5) and soluble thymidine kinase 1 (TK1) genes as near neighbours. Starting with human liver RNA, I was neither able to amplify any threonine aldolase transcripts using a variety of 5' and 3' RACE methods nor to detect any transcripts in a wide range of tissue and cell line cDNAs by RT-PCR. A search of the human EST database identified five potential EST transcripts scattered throughout the threonine aldolase gene, but they lack supporting evidence that they are truly transcribed sequences, being unspliced singletons. There is a potential polyadenylation signal site in the human threonine aldolase gene with good homology to the murine site. However, corresponding 3'UTR ESTs and SAGE tags are conspicuously absent from the databases leading to the conclusion that the GLY1 threonine aldolase gene is not transcribed in man.
Homology of serine/threonine dehydratase and serine dehydratase like-1 proteins in vertebrates
Expression of threonine aldolase, serine/threonine dehydratase and serine dehydratase like-1 mRNA in mouse tissues
Expression of threonine catabolic enzymes in mouse embryos
In vertebrates, L-threonine is one of the indispensable amino acids. It is obtained from protein in the diet, typically being the second or third limiting amino acid in herbivorous diets. Some of it is utilized in synthesising new protein, but the rest is converted to other amino acids by oxidative catabolism by three different enzymes that are found in most organisms; TDH, TA and SDH. Both the TDH and TA pathways produce glycine. However, the TDH pathway occurs in two steps, requiring KBL as the second step. Using protein homology searches of the mouse genome with the bacterial enzymes has allowed me to identify and clone TDH and KBL cDNAs [36, 37]. GLY1/TA genes have been identified previously in bacteria, fungi and plants [16, 21, 25]. Here I describe the first TA cDNA found in vertebrates. The murine TA cDNA encodes a 400-residue protein that is highly similar to that from T. maritima with an expect value of 2e-73, being clearly distinct from glycine dehydrogenase, the second most closely related protein, with an expect value of 0.002. This remarkable conservation, over billions of years of evolution since the last common ancestor, shows the general importance of these metabolic pathways. However, the presence of some abnormal TA mRNA splicing in mouse, the low levels of mRNA found in mouse tissues, together with the low levels of TA enzymatic activity found in rat liver [4, 15] plus the loss of a functional TA gene in humans suggests that TA has reduced importance in mammals.
The L-TA enzymes can act on the stereoisomers, L-threonine and L-allo-threonine. These can be divided into three types based on the stereospecificity towards the β-carbon of threonine. Low-specificity L-TA can use both L-threonine and L-allo-threonine as substrates. L-TA only acts on L-threonine and L-allo-TA is specific to L-allo-threonine . Murine L-TA is likely to be a low-specificity L-TA with a preferences for the allo isomer in a manner similar to the T. maritima enzyme, because Tyr127 (Tyr87 in T. maritima) in the TA active site is conserved, a residue which appears to be involved in discriminating L-threonine from L-allo-threonine .
All the vertebrate TA proteins have putative amino-terminal mitochondrial import sequences, suggesting that the mitochondrion is its intracellular localisation. In contrast, fractionation studies in the yeast, S. cerevisiae, revealed a cytosolic localisation for TA . Additionally, the yeast TA protein does not possess an amino-terminal mitochondrial import sequence. In vertebrates, threonine catabolism is mostly confined to the liver when the mass of the organ is taken into consideration. Expression of SDH, TDH and KBL mRNA are highest in liver [36, 37, 39]. However, low levels of murine TA expression were found in a wide range of tissues suggesting a role in housekeeping metabolism in all tissues. Generally, during embryogenesis, expression of threonine catabolic enzymes increased with maturation of the developing liver.
Humans have lost two of the three enzymes of threonine catabolism with both GLY1 and TDH  genes being defective, both pathways produce glycine from threonine. In man, the loss of a functional GLY1 gene appears to be a more ancient event than the loss of TDH because GLY1 genes in both man and chimpanzees have a number of frame-shifts and mutations of functional amino acid residues, whereas the mutated exon 6 splice-acceptor site in human TDH is intact in chimpanzees (data not shown). This suggests that GLY1 has been lost prior to, and TDH after, the divergence of man and chimpanzees, about 6–8 million years ago. Consequently, humans may not be as metabolically well equipped as other species to cope with diets high in threonine/protein. Perhaps a reduction in the rate of threonine catabolism in man's ancestors would have conferred a selective advantage on those individuals with these defective genes under conditions of protein starvation. Although humans have lost both the glycinergic pathways of threonine catabolism their gut microbial flora will have both TA and TDH enzymes, therefore, gut microbial flora may make significant contributions to human threonine catabolism.
With the loss of TA and TDH genes in humans this leaves serine/threonine dehydratase as our only major threonine catabolic enzyme. However, vertebrates also have a second SDH gene, called SDH-like-1 which, by homology, is likely to function also as a serine/threonine dehydratase since all the residues that bind the PLP co-factor are conserved between the two proteins. Only the SDH1 gene is present in the chicken, therefore the serine dehydratase activity found in chick livers  must be due to SDH1.
The SHMT enzymes are members of the α-class of pyridoxal phosphate enzymes, catalyzing the reversible interconversion of serine and glycine. Mammals have two SHMT genes. One encodes a cytosolic and the other a mitochondrial enzyme. Purified SHMT enzyme from rat liver possesses some threonine aldolase activity  and both SHMT genes may also contribute to threonine catabolism in vertebrates.
With the identification of murine TA and SDH-1 mRNA the way is open to study their enzymatic activity in vitro and relative contribution to threonine catabolism under different physiological states in vivo. Changes in TA and SDH-1 mRNA expression in response to diet have yet to be examined, but rats fed a high protein diet or fasted showed an increase in TA enzymatic activity . In contrast, quails and rats fasted or on threonine enriched diets did not show any statistically significant changes in TA enzymatic activity .
I have shown that GLY1/TA genes are present in vertebrates. TA genes and enzymatic activities have been previously isolated from bacteria, fungi and plants. These enzymes are distinct from the serine hydroxymethyltransferases. The mouse GLY1 gene is located on chromosome 11, band E2 and the 1855 bp cDNA from this gene encodes a 400-residue threonine aldolase. The presence of a positively-charged amino-terminal import leader peptide sequence in mammalian, amphibian and fish TA proteins, that are not present in bacterial proteins, suggests that the vertebrate TA enzymes are mitochondrial. Man and chimpanzees have lost a functional GLY1 gene. Vertebrates also have a second SDH gene, SDH1, that by homology to the crystal structure of SDH may function as a threonine dehydratase and contribute to threonine catabolism.
Molecular cloning of murine L-threonine aldolase
Total RNA was extracted from mouse liver using guanidine thiocyanate and treated with DNase-I to remove any contaminating genomic DNA (SV total RNA isolation system, Promega, UK). Total RNA was reversed transcribed with AMV RNase H- reverse transcriptase (ThermoScript, Life Technologies, UK) at 50°C using an oligo-dT primer. The cDNA was amplified by touchdown PCR using the Advantage cDNA polymerise mix (Clontech, UK) on a Perkin-Elmer 2400 thermocycler. Amplification conditions for the first 10 cycles were 94°C for 5 sec, 72°C less 0.4°C per cycle for 3 min and for the next 20 cycles 94°C for 5 sec, 68°C for 10 sec, 72°C for 3 min per cycle using primers (100 nM) derived from the sequence of the mouse genomic DNA from clone RP23-268N22 (accession number AL591433 forward 5'-ATAGTGCCCCGGGCTTGC-3' and, first reverse 5'-TTTTTTTTTTTTTTTGTGCCTTCAGTATTT-3' and (Amersham-Pharmacia Biotech, UK). PCR amplicons were electrophoresised in a low-melting point agarose gel stained with ethidium bromide. They were excised from the gel. The agarose digested with agarase (Promega, U.K.). These PCR amplicons were cloned into pCR-II-TOPO, a T-A vector (Invitrogen, The Netherlands) and sequenced in both directions using the big dye terminator cycle sequencing ready reaction kit with AmpliTaq DNA polymerase FS on an ABI 373XL Stretch Sequencer (both from PE Applied Biosystems, UK). SDH and SDH-1 cDNAs were cloned in a similar manner and were used as positive controls in RT-PCR assays.
Gene expression in mouse tissues by real time PCR
Quantitative PCR was carried out on a GeneAmp 5700 Sequence Detection System (AB Applied Biosystems) and a Rotor Gene 3000 utilising a CAS-1200 robotic precision liquid handling system (Corbett Research, Australia) using a SYBR Green I double-stranded DNA binding dye assay (Applied Biosystems, UK). For the determination of TA, SDH, SDH1, TDH and KBL mRNA expression in adult mouse tissues and whole mouse embryos, cDNAs were generated from polyA+ selected RNA by reverse transcriptase using an oligo-dT primer (BD Clontech, UK). Approximately 8.0 ng of cDNA were used for each PCR. Tissue master mixes were divided into gene specific mixes and primers were added to a final concentration of 200 μM. The primers were: TA, CCCAGAGATTCGCTAAAGGACTC (exon 6/7) and CACGGCCAGTCTGAGCCAC (exon 7), which produced a 171 bp amplicon; SDH, TTTTACGAACACCCCATTTTCTC (exon 7) and AGAATCTTCTCATCGTCCACGAA (exon 8/7), which produced an 89 bp amplicon; SDH1, CCTGCCAGACATCACCAGTGT (exon 6/7) and GCGCTCATCGTCCAGGAA (exon 8/7), which produced a 154 bp amplicon; G3PDH, TCCCACTCTTCCACCTTCGA and GTCCACCACCCTGTTGCTGTA, which produced a 111 bp amplicon. Primers for beta-actin, TDH and KBL have been described previously . Amplification conditions were; a 10 min hot start to activate the polymerase followed by up to 50 cycles of 95°C for 15 sec and 60°C for 1 min. The number of cycles required for the fluorescence to become significantly higher than background fluorescence (termed cycle threshold [Ct]) was used as a measure of abundance. A comparative Ct method was used to determine gene expression. Expression levels in each tissue cDNA sample were normalised to the average expression levels of the housekeeping genes beta-actin and G3PDH (ΔCt). Ratios of gene of interest mRNA/housekeeping mRNA from each tissue were standardised to that of the highest expressing tissue for that gene which was taken as 100% (ΔΔCt). Formula E-ΔΔCt was used to calculate relative expression levels where E is the efficiency of the PCR per cycle. Amplification specificity was confirmed by melting curve analysis and agarose gel electrophoresis.
The predicted start site of transcription of murine TA mRNA was determined using the program Eponine . The predicted secondary structure of the protein was determined using the Psi-Pred program  aligned with that of the crystal structure of TA from the bacteria T. maritima  using 3D-PSSM . Mitochondrial locations were predicted for the TA proteins using MITOPRED . Cleavage-sites in the mitochondrial targeting peptides were identified using PSORT .
I thank Cameron Tristan Edgar, Chloe Fiona Edgar and Maria-athina Milona for technical help with PCR and cloning, and June Edgar for her constructive comments on the manuscript, and the Advanced Biotechnology Centre, Charing Cross Campus, Imperial College for DNA sequencing.
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