Structural characterization of the rat malic enzyme gene

Alternative Polyadenylation of Malic Enzyme 1 Is Essential for Accelerated Adipogenesis

Understanding the mechanism of adipogenesis is an important basis for improving meat quality traits of livestock. Alternative polyadenylation (APA) is a vital mechanism to regulate the expression of eukaryotic genes. However, how the individual APA functions in adipogenesis remains elusive. This study was intended to investigate the effect of malic enzyme 1 (ME1) APA on adipogenesis. Here, intracellular lipid droplets were stained using Oil red O. 3' RACE was used to verify APA events of the ME1 gene. Interactions between ME1 3' untranslated region (3' UTR)-APA isoforms and miRNAs, as well as differential expression of isoforms, were examined using dual-luciferase reporter and molecular experiments. The mechanism of ME1 APA on adipogenesis was explored by gain and loss of function assays. In this study, two ME1 isoforms with different 3' UTR lengths were detected during adipogenesis. Moreover, the ME1 isoform with a short 3' UTR was significantly upregulated compared with the one with a long 3' UTR. Mechanistically, only the long ME1 isoform was targeted by miR-153-3p to attenuate adipogenesis, while the short one escaped the regulation of miR-153-3p to accelerate adipogenesis. Our results reveal a novel mechanism of ME1 APA in regulating adipogenesis.

Estradiol-17β: Tracing its metabolic significance in female fatbody of fifth instar larvae of silkworm, Bombyx mori L (race: Nistari)

In recent years, various vertebrate peptide and steroid hormones have been identified in invertebrates, estradiol-17beta (E2) being a major one. We have specifically shown NADP-malate dehydrogenase (NADP-MDH) activity in fifth instar larval fatbody of female silkworm, Bombyx mori, as an E2 responsive parameter. Interestingly enough, estradiol-induced increase in the enzyme activity could be counteracted by simultaneous application of specific E2-inhibitor, ICI-182780. Further, a nice correlation was obtained among the E2 titre, specific *E2 binding and expression of NADP-MDH activity in fatbody during different days of normal fifth instar larval development. Though the nature of the binding sites is quite similar to known steroid receptors of vertebrate, the reported absence of estrogen receptor gene in some insects poses a question. A recent finding regarding the presence of an estrogen-related receptor ortholog in fruit fly may provide some answers. The specific effects elicited by estradiol in the female fatbody of this insect support its possibility of having an important metabolic function. This role played by E2, whether hormonal or not, is yet to be identified.

Swine cytosolic malic enzyme: cDNA cloning, sequencing, and localization

A highly significant genetic association has been found between some alleles of the swine Major Histocompatibility Complex SLA (Swine Leukocyte Antigen genetic complex) and the cytosolic malic enzymatic activity level in muscles. The aim of this study was to find out whether this genetic association was due to a close linkage of the SLA region and the gene coding for the enzyme. Since no swine cytosolic malic enzyme sequence (ME1) was available, we isolated several overlapping fragments that spanned the almost entire malic enzyme transcript both by screening of a swine cDNA library and by RT-PCR. The results indicated the existence of two transcripts of 2. 0 and 3.1 kb, which probably correspond to two alternative forms of one gene. The sequence of the transcript was highly similar to the other published mammalian cytosolic NADP+-dependent malic enzyme cDNA, especially within the four functional domains. Two major bands at 3.7 and 2.4 kb were detected on Northern blots containing the RNA from 25 tissues from fetuses and adult pigs. A high expression level was found in the adrenal gland, muscle, liver, and peripheral nerves. The analysis of malic enzyme RFLPs in five SLA informative families revealed an independent segregation of the ME1 gene from the SLA region. In situ hybridization results localized the cytosolic malic enzyme on the swine Chromosome (Chr) 1p1.2, except that the association between SLA and the malic enzyme activity level was due to a physical genetic linkage. Thus, the mechanisms underlying this association remain to be elucidated.

Identification of direct-repeat-binding protein 1 (DRP-1), a DNA-binding protein that binds specifically to the 'malic' enzyme gene promoter direct repeat element

The 'malic' enzyme (ME) gene promoter contains three main regulatory regions. One of these, the direct repeat element (DRE), contains tandem degenerate Sp1-binding sites separated by a 3 bp intervening sequence. We now show that a previously unreported 95 kDa protein, which we have designated DRP-1, binds strongly to the DRE region in a highly specific manner. Western-blot analysis confirms that this protein is not Sp1, which has been shown to bind to similar degenerate sites. Competitive binding assays using purified DRP-1 further reveal that neither non-specific nor Sp1-consensus-site-containing oligonucleotides can displace those complexes formed between DRP-1 and the DRE sequence, thus confirming sequence-specific binding by this protein. SDS/PAGE analysis of DRE-protein complexes isolated by direct excision and transplantation from retardation gels confirms the presence of the 95 kDa protein and, in addition, suggests that more than one binding site exists for this protein within the DRE. This is in accord with the repeated nature of the DRE DNA sequence which contains two CACC box motifs.

Primary structure of the hydrogenosomal malic enzyme of Trichomonas vaginalis and its relationship to homologous enzymes

The complete nucleotide sequence has been established for two genes (maeA and maeB) coding for different subunits of the hydrogenosomal malic enzyme [malate dehydrogenase (decarboxylating) EC 1.1.1.39] of Trichomonas vaginalis. Two further genes (maeC and maeD) of this enzyme have been partially sequenced. The complete open reading frames code for polypeptides of 567 amino acids in length. These two open reading frames are similar with less than 12 percent pairwise nucleotide differences and less than 9 percent pairwise amino acid differences. The open reading frames of the two partially sequenced genes correspond to the amino-terminal part of the polypeptides coded and are similar to the corresponding parts of the completely sequenced ones. The deduced translation products of the two complete genes differ in their calculated pI values by 1.5 pH unit. The genes code for polypeptides which contain 12 or 11 amino-terminal amino-acyl residues not present in the proteins isolated from the cell. Other hydrogenosomal enzymes also have similar amino-terminal extensions which probably play a role in organellar targeting and translocation of the newly synthesized polypeptides. A comparison of 19 related enzymes from bacteria and eukaryotes with the maeA product revealed 34-45 percent amino acid identity. Phylogenetic reconstruction based on nonconservative amino acid differences with maximum parsimony (phylogenetic analysis using parsimony, PAUP) and distance based (neighbor-joining, NJ) methods showed that the T. vaginalis enzyme is the most divergent of all eukaryotic malic enzymes, indicating its long independent evolutionary history.

Characterization of a bean (Phaseolus vulgaris L.) malic-enzyme gene

We have isolated a genomic clone encoding a plant NADP(+)-dependent malic enzyme (NADP-ME). This clone, isolated from bean (Phaseolus vulgaris L.), covers the entire gene (exons, introns) and 5'-flanking regions. DNA sequencing defines 20 exons spanning approximately 4.5 kb, which range over 48-235 bp in size. All 19 introns are fairly small (79-391). The first intron resides in the 5'-untranslated leader sequence. Introns 10, 11 and 16 are located at positions identical to a rat malic-enzyme gene. In the promoter region, a TATA box (TATATATA) is easily recognized 41 bp upstream of a single transcription-initiation site. Two potential cis-acting elements with homology to elements from plant genes, activated by UV light and fungal elicitors, were identified at positions -153 and -312, respectively. Southern-blot analysis suggests a single gene copy, but also other distantly related genes, in the bean genome. The deduced NADP-ME protein of 589 amino acids exhibits features consistent with a cytoplasmic location. We describe the organization of the NADP-ME protein into functional domains located on separate exons. The evolution of malic-enzyme genes coding for isoforms in different cellular compartments of plants and animals is discussed.

Molecular analysis of the malic enzyme gene (mae2) of Schizosaccharomyces pombe

Sequence analysis of a 4.6-kb HindIII fragment containing the malic enzyme gene (mae2) of Schizosaccharomyces pombe, revealed the presence of an open reading frame of 1695 nucleotides, coding for a 565 amino acid polypeptide. The mae2 gene is expressed constitutively and encodes a single mRNA transcript of 2.0 kb. The mae2 gene was mapped on chromosome III by chromoblotting. The coding region and inferred amino acid sequence showed significant homology with 12 malic enzyme genes and proteins from widely different origins. Eight highly homologous regions were found in these malic enzymes, suggesting that they contain functionally conserved amino acid sequences that are indispensable for activity of malic enzymes. Two of these regions have previously been reported to be NAD- and NADP-binding sites.

Duck liver 'malic' enzyme. Expression in Escherichia coli and characterization of the wild-type enzyme and site-directed mutants

A cDNA for duck liver 'malic' enzyme (EC 1.1.1.40) was subcloned into pUC-8, and the active enzyme was expressed in Escherichia coli TG-2 cells as a fusion protein including a 15-residue N-terminal leader from beta-galactosidase coded by the lacZ' gene. C99S and R70Q mutants of the enzyme were generated by the M13 mismatch technique. The recombinant enzymes were purified to near homogeneity by a simple two-step procedure and characterized relative to the enzyme isolated from duck liver. The natural duck enzyme has a subunit molecular mass of approx. 65 kDa, and the following kinetic parameters for oxidative decarboxylation of L-malate at pH 7.0: Km NADP+ (4.6 microM); Km L-malate (73 microM); kcat (160 s-1); Ka (2.4 microM) and Ka' (270 microM), dissociation constants of Mn2+ at 'tight' (activating) and 'weak' metal sites; and substrate inhibition (51% of kcat. at 8 mM-L-malate). Properties of the E. coli-derived recombinant wild-type enzyme are indistinguishable from those of the natural duck enzyme. Kinetic parameters of the R70Q mutant are relatively unaltered, indicating that Arg-70 is not required for the reaction. The C99S mutant has unchanged Km for NADP+ and parameters for the 'weak' sites (i.e. inhibition by L-malate, Ka'); however, kcat. decreased 3-fold and Km for L-malate and Ka each increased 4-fold, resulting in a catalytic efficiency [kcat./(Km NADP+ x Km L-malate x Ka)] equal to 3.7% of the natural duck enzyme. These results suggest that the positioning of Cys-99 in the sequence is important for proper binding of L-malate and bivalent metal ions.

Pre-translational control of hepatic malic enzyme expression during the development of the rat

The expression of hepatic cytosolic malic enzyme in the developing rat has been studied by molecular-biological techniques. Malic enzyme mRNA was barely detectable throughout the neonatal period, but increased to significant levels immediately before weaning. Northern-blot analysis demonstrated that the two major malic enzyme mRNA species displayed non-co-ordinate control during development, with the 2.0 kb form accumulating to a greater extent than the 3.1 kb form. A novel 1.6 kb mRNA species was found to predominate in foetal samples. Tri-iodothyronine treatment of neonatal rats caused premature induction of all three malic enzyme mRNA species. Dietary studies also showed precocious induction of the mRNA with diets high in carbohydrate, but not with those high in fat.

Cloning and sequence of the human adrenodoxin reductase gene

Adrenodoxin reductase (ferrodoxin:NADP+ oxidoreductase, EC 1.18.1.2) is a flavoprotein mediating electron transport to all mitochondrial forms of cytochrome P450. We cloned the human adrenodoxin reductase gene and characterized it by restriction endonuclease mapping and DNA sequencing. The entire gene is approximately 12 kilobases long and consists of 12 exons. The first exon encodes the first 26 of the 32 amino acids of the signal peptide, and the second exon encodes the remainder of signal peptide and the apparent FAD binding site. The remaining 10 exons are clustered in a region of only 4.3 kilobases, separated from the first two exons by a large intron of about 5.6 kilobases. Two forms of human adrenodoxin reductase mRNA, differing by the presence or absence of 18 bases in the middle of the sequence, arise from alternate splicing at the 5' end of exon 7. This alternately spliced region is directly adjacent to the NADPH binding site, which is entirely contained in exon 6. The immediate 5' flanking region lacks TATA and CAAT boxes; however, this region is rich in G + C and contains six copies of the sequence GGGCGGG, resembling promoter sequences of "housekeeping" genes. RNase protection experiments show that transcription is initiated from multiple sites in the 5' flanking region, located about 21-91 base pairs upstream from the AUG translational initiation codon.