Crystallization and preliminary X-ray study of recombinant betaine-homocysteine S-methyltransferase from rat liver

Betaine homocysteine S-methyltransferase emerges as a new player of the nuclear methionine cycle

The paradigm of a cytoplasmic methionine cycle synthesizing/eliminating metabolites that are transported into/out of the nucleus as required has been challenged by detection of significant nuclear levels of several enzymes of this pathway. Here, we show betaine homocysteine S-methyltransferase (BHMT), an enzyme that exerts a dual function in maintenance of methionine levels and osmoregulation, as a new component of the nuclear branch of the cycle. In most tissues, low expression of Bhmt coincides with a preferential nuclear localization of the protein. Conversely, the liver, with very high Bhmt expression levels, presents a main cytoplasmic localization. Nuclear BHMT is an active homotetramer in normal liver, although the total enzyme activity in this fraction is markedly lower than in the cytosol. N-terminal basic residues play a role in cytoplasmic retention and the ratio of glutathione species regulates nucleocytoplasmic distribution. The oxidative stress associated with d-galactosamine (Gal) or buthionine sulfoximine (BSO) treatments induces BHMT nuclear translocation, an effect that is prevented by administration of N-acetylcysteine (NAC) and glutathione ethyl ester (EGSH), respectively. Unexpectedly, the hepatic nuclear accumulation induced by Gal associates with reduced nuclear BHMT activity and a trend towards increased protein homocysteinylation. Overall, our results support the involvement of BHMT in nuclear homocysteine remethylation, although moonlighting roles unrelated to its enzymatic activity in this compartment cannot be excluded.

Molecular characterization and analysis of the porcine betaine homocysteine methyltransferase and betaine homocysteine methyltransferase-2 genes

Betaine homocysteine methyltransferase (BHMT) and BHMT-2 enzymes methylate homocysteine to form methionine using betaine and S-methylmethionine, respectively. These activities are observed only in the liver of adult rodents, but in adult humans and pigs these activities are detected in both the liver and kidney, indicating the pig is a more appropriate model for studying the biochemical and physiological roles of these enzymes in human biology. Porcine BHMT and BHMT-2 cDNAs were cloned and sequenced, and their 5' and 3' UTR were amplified using RLM-RACE. The BHMT transcript had significantly longer 5' and 3' UTRs than BHMT-2. The pig BHMT and BHMT-2 genes span approximately 26 and 16kb, respectively, and both genes have 8 exons. The deduced amino acid sequences of BHMT and BHMT-2 contain 407 and 363 amino acids, respectively, and shared 78% amino acid identity. No promoter element (TATA or CAAT box) was observed for either BHMT or BHMT-2, although a CpG island surrounding the promoter and transcriptional start site was observed in both genes implying that methylation could regulate their expression. Using qPCR, it was determined that BHMT and BHMT-2 transcripts are very abundant in liver and kidney cortex, whereas the expression is significantly less in other tissues. These findings confirm that the expression pattern of BHMT and BHMT-2 genes in pigs is similar to humans, supporting the use of the pig as an animal model to study the genetics and regulation of BHMT and BHMT-2 expression.

Human betaine-homocysteine methyltransferase (BHMT) and BHMT2: common gene sequence variation and functional characterization

Betaine-homocysteine methyltransferase (BHMT) catalyzes the remethylation of homocysteine. BHMT2 encodes a protein 73% identical in amino acid sequence to BHMT, but the function of BHMT2 remains unclear. We set out to identify and functionally characterize common genetic variation in BHMT and BHMT2. Specifically, we sequenced exons, exon-intron splice junctions and the 5'-flanking regions (5'-FRs) of BHMT and BHMT2 using 240 DNA samples from four ethnic groups. Twenty-five single nucleotide polymorphisms (SNPs), including 4 nonsynonymous SNPs, and 39 SNPs, including 4 nonsynonymous, were observed in BHMT and BHMT2, respectively. BHMT wild type (WT) and variant allozymes were expressed in COS-1 cells. Variant allozymes showed no significant differences from WT in levels of enzyme activity or immunoreactive protein, but there were statistically significant differences in apparent K(m) values. Luciferase reporter gene constructs were created for the three most common BHMT 5'-FR haplotypes, and significant variation was observed in the ability of these constructs to drive transcription. Although BHMT2 mRNA has been observed in human liver and kidney, expression of the protein has not been reported. We were unable to express BHMT2 in mammalian cells, and the protein aggregated after bacterial expression. Furthermore, BHMT2 was rapidly degraded in a rabbit reticulocyte lysate, but it could be stabilized by cotransfection of COS-1 cells with BHMT and, after cotransfection, it coprecipitated with BHMT. These studies have defined common genetic variation in BHMT and BHMT2 and functionally characterized BHMT SNPs. They may also help to explain why BHMT2 has not previously been defined functionally.

Rat liver betaine-homocysteine S-methyltransferase equilibrium unfolding: insights into intermediate structure through tryptophan substitutions

Equilibrium folding of rat liver BHMT (betaine-homocysteine methyltransferase), a TIM (triosephosphate isomerase)-barrel tetrameric protein, has been studied using urea as denaturant. A combination of activity measurements, tryptophan fluorescence, CD and sedimentation-velocity studies suggested a multiphasic process including two intermediates, a tetramer (I4) and a monomer (J). Analysis of denaturation curves for single- and six-tryptophan mutants indicated that the main changes leading to the tetrameric intermediate are related to alterations in the helix alpha4 of the barrel, as well as in the dimerization arm. Further dissociation to intermediate J included changes in the loop connecting the C-terminal alpha-helix of contact between dimers, disruption of helix alpha4, and initial alterations in helix alpha7 of the barrel, as well as in the dimerization arm. Evolution of the monomeric intermediate continued through additional perturbations in helix alpha7 of the barrel and the C-terminal loop. Our data highlight the essential role of the C-terminal helix in dimer-dimer binding through its contribution to the increased stability shown by BHMT as compared with other TIM barrel proteins. The results are discussed in the light of the high sequence conservation shown by betaine-homocysteine methyltransferases and the knowledge available for other TIM-barrel proteins.

Oligomerization is required for betaine-homocysteine S-methyltransferase function

Betaine-homocysteine methyltransferase (BHMT) is a member of a family (Pfam 02574) of zinc- and thiol/selenol-dependent methyltransferases. All family members purified to date are monomers, except BHMT, which is an oligomer. We have studied how C-terminal truncation or mutagenic replacement of residues within or associated with the unique dimerization arm of this enzyme affects oligomerization and function. Two C-terminal truncation mutants, S325 and D371, do not express well in Escherichia coli and are inactive. Residues within the dimerization arm (H338, R346, W352, R361, P362, Y363, N364, and P365) and one that forms a hydrogen bond to the arm (E266) were changed to alanine. All mutants maintained a normal or near-normal ability to bind zinc. E266A, R361A, P362A, Y363A, N364A, and P365A displayed near-normal catalytic activity, but H338A had only 10% of the wild-type enzyme activity. Like the wild-type enzyme, most mutants eluted as tetramers from gel filtration columns and formed discrete bands on SDS-PAGE gels following glutaraldehyde crosslinking. Mutants R346A and W352A had negligible activity, eluted as dimers, and displayed aberrant crosslinking properties. These data indicate that unlike other Pfam 02574 members, oligomerization of BHMT is required for function.

Crystal Structure of Rat Liver Betaine Homocysteine S-Methyltransferase Reveals New Oligomerization Features and Conformational Changes Upon Substrate Binding

Betaine homocysteine S-methyltransferase (BHMT) is one of the two enzymes known to methylate homocysteine to generate methionine in the liver. It presents a Zn(2+) atom linked to three essential Cys residues. The crystal structure of rat liver BHMT has been solved at 2.5A resolution, using crystals with P2(1) symmetry and 45% solvent content in the cell. The asymmetric unit contains the whole functional tetramer showing point symmetry 222. The overall fold of the subunit consists mostly of a (alpha/beta)(8) barrel, as for human BHMT. From the end of the barrel, the polypeptide chain extends away and makes many interactions with a different subunit, forming tight dimers. The most remarkable structural feature of rat liver BHMT is the presence of a helix including residues 381-407, at the C terminus of the chain, which bind together the dimers AB to CD. A strong ion-pair and more than 60 hydrophobic interactions keep this helix stacked to the segment 316-349 from the opposite subunit. Moreover, the crystal structure of free rat liver BHMT clearly shows that Tyr160 is the fourth ligand coordinated to Zn, which is replaced by Hcy upon binding. Two residues essential for substrate recognition, Phe76 and Tyr77, are provided by a conformational change in a partially disordered loop (L2). The crucial role of these residues is highlighted by site-directed mutagenesis.

Active-site-mutagenesis study of rat liver betaine-homocysteine S-methyltransferase

A site-directed-mutagenesis study of putative active-site residues in rat liver betaine-homocysteine S-methyltransferase has been carried out. Identification of these amino acids was based on data derived from a structural model of the enzyme. No alterations in the CD spectra or the gel-filtration chromatography elution pattern were observed with the mutants, thus suggesting no modification in the secondary structure content or in the association state of the proteins. All the mutants obtained showed a reduction of the enzyme activity, the most dramatic effect being that of Glu(159), followed by Tyr(77) and Asp(26). Changes in affinity for either of the substrates, homocysteine or betaine, were detected when substitutions were performed of Glu(21), Asp(26), Phe(74) and Cys(186). Interestingly, Asp(26), postulated to be involved in homocysteine binding, has a strong effect on affinity for betaine. The relevance of these results is discussed in the light of very recent structural data obtained for the human enzyme.