Expression of three mRNA species from a single rat aldolase A gene, differing in their 5' non-coding regions

A developmental biological study of aldolase gene expression in Xenopus laevis

We cloned cDNAs for Xenopus aldolases A, B and C. These three aldolase genes are localized on different chromosomes as a single copy gene. In the adult, the aldolase A gene is expressed extensively in muscle tissues, whereas the aldolase B gene is expressed strongly in kidney, liver, stomach and intestine, while the aldolase C gene is expressed in brain, heart and ovary. In oocytes aldolase A and C mRNAs, but not aldolase B mRNA, are extensively transcribed. Thus, aldolase A and C mRNAs, but not B mRNA, occur abundantly in eggs as maternal mRNAs, and strong expression of aldolase B mRNA is seen only after the late neurula stage. We conclude that aldolase A and C mRNAs are major aldolase mRNAs in early stages of Xenopus embryogenesis which proceeds utilizing yolk as the only energy source. aldolase B mRNA, on the other hand, is expressed only later in development in tissues which are required for dietary fructose metabolism. We also isolated the Xenopus aldolase C genomic gene (ca. 12 kb) and found that its promoter (ca. 2 kb) contains regions necessary for tissue-specific expression and also a GC rich region which is essential for basal transcriptional activity.

Coregulation of fast contractile protein transgene and glycolytic enzyme expression in mouse skeletal muscle

Little is known of the gene regulatory mechanisms that coordinate the contractile and metabolic specializations of skeletal muscle fibers. Here we report a novel connection between fast isoform contractile protein transgene and glycolytic enzyme expression. In quantitative histochemical studies of transgenic mouse muscle fibers, we found extensive coregulation of the glycolytic enzyme glycerol-3-phosphate dehydrogenase (GPDH) and transgene constructs based on the fast skeletal muscle troponin I (TnIfast) gene. In addition to a common IIB > IIX > IIA fiber type pattern, TnIfast transgenes and GPDH showed correlated fiber-to-fiber variation within each fast fiber type, concerted emergence of high-level expression during early postnatal muscle maturation, and parallel responses to muscle under- or overloading. Regulatory information for GPDH-coregulated expression is carried by the TnIfast first-intron enhancer (IRE). These results identify an unexpected contractile/metabolic gene regulatory link that is amenable to further molecular characterization. They also raise the possibility that the equal expression in all fast fiber types observed for the endogenous TnIfast gene may be driven by different metabolically coordinated mechanisms in glycolytic (IIB) vs. oxidative (IIA) fast fibers.

Molecular evolution of Aldolase A pseudogenes in mice: multiple origins, subsequent duplications, and heterogeneity of evolutionary rates

The Aldolase multigene family comprises three functional genes (A, B, and C) with tissue-specific expression regulated during ontogeny. DGGE analysis and nucleotide sequencing reveal a family of retropseudogenes of type A in species of MUS: Significant variation in rates of evolution of Aldolase A retropseudogenes is apparent. Our analyses demonstrate that (1) multiple events of retrotransposition are needed to account for the diversity of Aldolase A processed pseudogenes found in mice; (2) some of these sequences have undergone further duplication subsequent to the original retrotransposition event; (3) the patterns of nucleotide substitution are broadly comparable with previous estimates; and (4) estimates of rates of divergence for this array of sequences are up to four times higher than those reported in the literature.

Functional studies by site-directed mutagenesis on the role of Sp1 in the expression of the pyruvate kinase M and aldolase A genes

During the cell cycle of mitogen stimulated rat thymocytes, an 8-10-fold induction of glycolytic enzymes and a corresponding increase in the mRNA levels has been observed. This prompted us to study the transcriptional regulation of the rat aldolase A and pyruvate kinase M genes. cis-Regulatory elements of both promoters were evaluated by site-directed mutagenesis of promoter/luciferase constructs and transient transfections of rat hepatoma FTO2B cells. Furthermore, the binding proteins were identified by mobility shift assays in the presence of specific antibodies. In the aldolase AH1 promoter, five binding sites for Sp1 and Sp3 and a TPA responsive element were identified as essential for transcriptional regulation. Most of the promoter activity can be attributed to these regulatory elements. In the pyruvate kinase M promoter three out of five binding sites of Sp1 and Sp3 (B box and GC boxes 1 and 3) turned out to be functional in the transfection assays whereas the disruption of GC box 2 had no effect, and the disruption of the GC box 4 had only a minor effect on the promoter activity. Both promoters are stimulated by Sp1 as well as Sp3, as judged by cotransfection experiments of Drosophila SL2 cells. Therefore, the Sp1- and Sp3-directed transcription provides a means for common regulatory mechanism of the aldolase A and the pyruvate kinase M genes.

Cloning of the Xenopus laevis aldolase C gene and analysis of its promoter function in developing Xenopus embryos and A6 cells

A Xenopus aldolase C gene (XAClambda3-1), much longer (9.6 kb) than human and rat genes (3.7-3.6 kb), was isolated and characterized, and expression studies were performed using Xenopus embryos and A6 cells, a kidney cell line constitutively expressing aldolase C gene. The Xenopus gene contained nine exons, and in its proximal 5'-upstream region a GC box and a 16 bp long aldolase C-specific element (ACSE), and in addition, a CCAAT box and a TATA-like element, both missing in mammalian genes. The lacZ gene connected to the 5'-upstream region (1.6 kb) of the aldolase gene containing many potentially regulative sequence elements was expressed in embryos temporally and spatially like the endogenous aldolase C gene. Deletion experiments using embryos and A6 cells suggested that this 5'-upstream DNA contained in its distal part a region which negatively affected on its expression in embryos, but not in A6 cells. The proximal-most region contained a basal promoter (68 bp) essential for expression in both embryos and A6 cells. Deletion experiments using A6 cells failed to detect such regulative regions within the first intron (spanning ca. 4 kb). Analyses with mutated promoters in A6 cells revealed that the GC box was the crucial element in the basal promoter, although the TATA-like element appeared to have a slightly stimulative effect on the GC box functioning. Gel retardation and foot-printing assays revealed the occurrence in A6 cells of a nuclear factor(s) that binds specifically to the GC box. Since Xenopus aldolase C gene has several unique structural features, we expect that it will provide an interesting material for studying the evolution and developmental control of the aldolase C gene.

Genomic sequences of aldolase C (Zebrin II) direct lacZ expression exclusively in non-neuronal cells of transgenic mice

Aldolase C is regarded as the brain-specific form of fructose-1, 6-bisphosphate aldolase whereas aldolase A is regarded as muscle-specific. In situ hybridization of mouse central nervous system using isozyme-specific probes revealed that aldolase A and C are expressed in complementary cell types. With the exception of cerebellar Purkinje cells, aldolase A mRNA is found in neurons; aldolase C message is detected in astrocytes, some cells of the pia mater, and Purkinje cells. We isolated aldolase C genomic clones that span the entire protein coding region from 1.5 kb 5' to the transcription start site to 0.5 kb 3' to the end of the last exon. The bacterial gene, lacZ, was inserted in two different locations and the constructs tested in transgenic mice. When the protein coding sequences were replaced with lacZ, three of five transgenic lines expressed beta-galactosidase only in cells of the pia mater; one line also expressed in astrocyte-like cells. When lacZ was inserted into the final exon (and all structural gene sequences were retained) transgene expression was observed in astrocytes in all regions of the central nervous system as well as in pial cells. Thus, with the exception of Purkinje cell expression, the behavior of the full-length transgene mimics the endogenous aldolase C gene. The results with the shorter transgene suggest that additional enhancer elements exist within the intragenic sequences. The absence of Purkinje cell staining suggests that the cis elements required for this expression must be located outside of the sequences used in this study.

Structure of aldolase A (muscle-type) cDNA and its regulated expression in oocytes, embryos and adult tissues of Xenopus laevis

We obtained cDNA (XALDA; 1466 bp) for Xenopus laevis aldolase A gene (muscle-type), whose amino acid sequence had 88% similarity to those of mammalian aldolase A genes. XALDA mRNA occurred abundantly in skeletal muscle and at low levels also in other adult tissues, and such mRNA distribution was reflected in zymograms. In oocytes XALDA mRNA occurred at a relatively high level from stage I, and the mRNA level peaked at stage II, then decreased in later stages. XALDA mRNA in the full-grown oocyte was inherited as maternal mRNA throughout maturation and fertilization until midblastula stage, but its level became very low during gastrula and early neurula stages, and then increased greatly in later stages. While maternal XALDA mRNA was distributed uniformly in early embryos, mRNA zygotically expressed after late neurula stage occurred mainly in somites. In blastula animal caps XALDA mRNA occurred at a low level, but the expression was greatly enhanced by activin treatment. Thus, in Xenopus laevis aldolase A gene is actively transcribed in earlier phase of oogenesis, inherited as maternal mRNA in early embryos in a cell-type nonspecific way, then in later phases of embryogenesis, it is strongly expressed in somites with its concomitant ubiquitous expression at low levels in almost all the other cell types.

Glucose regulates the promoter activity of aldolase A and pyruvate kinase M2 via dephosphorylation of Sp1

Proliferating cells and tumour cells maintain a high glycolytic rate even under aerobic conditions. FTO2B cells, a rat hepatoma cell line, show high activities of glycolytic enzymes. Within a culture period of 48 h the cell number increases 5-fold. Replacement of glucose by pyruvate in the culture medium lowers glycolytic enzyme activity and prevents proliferation. Transfection assays revealed that glucose deprivation dramatically decreases the transcriptional activities of the Sp1-dependent aldolase and pyruvate kinase promoters leading to reduced reporter gene expression. Sp1 binding activity is also inhibited by ocadaic acid, an inhibitor of protein phosphatase 1. Western blot analyses with nuclear extracts from FTO2B cells cultured in the presence or absence of glucose revealed differences in the phosphorylation state of Sp1. From these results we conclude that glucose increases the amount of the dephosphorylated form of Sp1 which has a higher DNA binding activity. As a consequence gene expression of the glycolytic enzymes is increased which is a prerequisite for cell proliferation.

Rapamycin inhibits aldolase A expression during human lymphocyte activation

Rapamycin (RAPA) strongly inhibits lymphocyte activation and proliferation, but does not affect most of the activation-related gene expression at the mRNA level. In order to understand the mechanism of action of RAPA and to gain further insights in lymphocyte signalling which is impaired by RAPA, we screened for RAPA-sensitive genes using differential hybridization. The expression of human aldolase A gene was found to be inducible during T and B cell activation, and the induction was repressed by RAPA at both the mRNA and enzymatic levels. The other two important immunosuppressants, cyclosporin A and FK506, also inhibited the mitogen-induced upregulation. However, none of these three drugs inhibited the constitutive expression. There was no fluctuation of aldolase A expression during the cell cycle, and RAPA failed to block the first cell cycle after synchronization in Jurkat cells. However, the second cycle was hampered by RAPA, and this was correlated with the inhibition of aldolase A expression during this later stage. Since aldolase A is a key enzyme in glycolysis and lymphocytes mainly depend on glycolysis for energy supply, the data from this study suggest that aldolase A might be one of the downstream targets of RAPA. The inhibition of the enzyme upregulation might deprive the cells of additional supply of energy, and prevent the cells from entering an optimal status for proliferation.

Differences in DNA-binding efficiency of Sp1 to aldolase and pyruvate kinase promoter correlate with altered redox states in resting and proliferating rat thymocytes

Thymocytes induce their glycolytic enzymes as they undergo transition from the resting to the proliferating state. Corresponding increases in mRNA levels point to a transcriptional regulation. Electrophoretic mobility shift assays revealed that the DNA-binding efficiency of Sp1 is increased when nuclear extracts from proliferating compared to resting rat thymocytes were used. Here we demonstrate that hydrogen peroxide, added to nuclear extract from proliferating cells, decreases the Sp1 DNA-binding activity, whereas in nuclear extracts from resting cells dithioerythritol fully restores DNA-binding efficiency. Moreover we show that in contrast to resting thymocytes, production of reactive peroxide anions upon priming with phorbol 12-myristate 13-acetate is nearly abolished in the proliferating cells. From these results we propose that reactive oxygen intermediates affect the interaction of the Sp1 transcription factor with its consensus sequence and subsequently regulate glycolytic gene expression.

The plastid aldolase gene from Chlamydomonas reinhardtii: intron/exon organization, evolution, and promoter structure

Genomic clones encoding the plastidic fructose-1,6-bisphosphate aldolase of Chlamydomonas reinhardtii were isolated and sequenced. The gene contains three introns which are located within the coding sequence for the mature protein. No introns are located within or near the sequence encoding the transit-peptide, in contrast to the genes for plastidic aldolases of higher plants. Neither the number nor the positions of the three introns of the C. reinhardtii aldolase gene are conserved in the plastidic or cytosolic aldolase genes of higher plants and animals. The 5' border sequences of introns in the aldolase gene of C. reinhardtii exhibit the conserved plant consensus sequence. The 3' acceptor splice sites for introns 1 and 3 show much less similarity to the eukaryotic consensus sequences than do those of intron 2. The plastidic aldolase gene has two tandemly repeated CAAT box motifs in the promoter region. Genomic Southern blots indicate that the gene is encoded by a single locus in the C. reinhardtii genome.

Noncoordinate changes in the steady-state mRNA expressed from aldolase A and aldolase C genes during differentiation of chicken myoblasts

In chickens, as in all vertebrates, tissue-specific expression of aldolase isozymes A, B, and C is developmentally coordinated. These developmental transitions in aldolase expression have been studied most extensively by charting enzyme activity during normal and abnormal development of specific vertebrate tissues. Indeed, aldolase expression has been a key marker for normal differentiation and for retrodifferentiation during carcinogenesis. Aldolase expression during chicken myoblast differentiation offers a model for investigating the regulatory mechanisms of these developmental transitions at the level of gene expression. For these studies, cDNAs encoding the most isozyme-specific regions of both chicken aldolase A and C were cloned. The chicken aldolase A cDNA represents the first report of this sequence. Aldolase steady-state mRNA expression was measured during chicken myoblast differentiation in primary cultures using RNase protection assays with cRNA probes generated from these aldolase cDNA clones. Steady-state mRNA for aldolase C, the predominant embryonic aldolase isozyme in chickens, did not significantly change throughout myoblast differentiation. In contrast, expression of steady-state mRNA for aldolase A, the only aldolase isozyme found in adult-skeletal muscle, was not detected until after myoblast fusion was approximately 50% completed. Aldolase A expression gradually increased throughout myoblast differentiation until approximately 48 h after fusion was completed when there was a dramatic increase. These results are contrasted with those of Turner et al. (1974) [Dev Biol 37:63-89] that showed a coordinated switch in isozyme activities between the embryonic aldolase C and the muscle-specific aldolase A. This discordant expression indicates that the aldolase A and C genes may employ different regulatory mechanisms during myoblast differentiation.

Expression of glycolytic isozymes in rat thymocytes during cell cycle progression

The time courses of activities of aldolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase and pyruvate kinase were determined in stimulated rat thymocytes at 24 h intervals during a period of 72 h of culture. In parallel the mRNA levels of these enzymes were analysed by Northern blotting with specific probes. Both the enzyme activities and the corresponding mRNA levels reached their maxima 48 h after stimulation coinciding with the S-phase of the cell cycle. The isozyme types of aldolase and hexokinase in resting and in mitogen-stimulated rat thymocytes were identified by Northern blot hybridisation using isozyme-specific probes. In these cells the aldolase A is expressed, whereas type B and C could not be detected. The transcription of the aldolase A gene can be regulated by two different promoters. Depending on the alternative usage of the promoters the aldolase A-specific mRNA either contains the non-translated exons M1 or AH1. In rat thymocytes the promoter proximal to the exon AH1 is used while the expression of mRNA I, the type characteristic for muscle tissue, was not observed. In contrast to aldolase two isozyme types of hexokinase were detected. Hexokinase I as well as hexokinase II were present in thymocytes whereas hexokinase III was not detectable. A shift in the isozyme pattern was not observed during the cell cycle progression.

Cloning of a brain-type aldolase cDNA and changes in its mRNA level during oogenesis and early embryogenesis in Xenopus laevis

A full length cDNA clone (cXALD3) for Xenopus laevis aldolase mRNA, which exists abundantly in oocytes, was isolated from Xenopus laevis ovary cDNA library, and its nucleotide sequence was determined. The cDNA was 1.8 kb in length and encoded 363 amino acids. From the deduced amino acid sequence and the Northern blot analysis of the RNAs from several adult tissues, this clone was concluded to be a brain-type aldolase gene. The XALD3 mRNA level per egg or embryo was high during early oogenesis, but was markedly reduced during late oogenesis and was maintained at low level during early embryogenesis until it started to increase at the late neurula stage. The mRNA was also detected in testis. The characteristic change in the temporal pattern of expression and the distribution of XALD3 mRNA among different tissues suggest a possibility that brain type aldolase may play some important roles in gametogenesis and in neurulation.

The MEF-3 motif is required for MEF-2-mediated skeletal muscle-specific induction of the rat aldolase A gene

The rat aldolase A gene contains two alternative promoters and two alternative first exons. The distal promoter M is expressed at a high level only in skeletal muscle. Previous in vitro transfection studies identified the region from -202 to -85 as an enhancer that is responsible for dramatic activation during the differentiation of chicken primary myoblasts. This enhancer contains an A/T-rich sequence resembling the MEF-2 motif, which is an important element of muscle enhancers and promoters. In this study, we demonstrate that the MEF-2 sequence is essential but not sufficient for the activity of the enhancer. Another region required for the activity was recognized by a nuclear factor, tentatively named MAF1. MAF1 was found in both muscle cells and nonmuscle cells, and MAF1 from both cell types was indistinguishable by gel retardation and DNase I footprint experiments. The sequence required for MAF1 binding is very similar to the MEF-3 motif, which is an element of the skeletal muscle-specific enhancer of the cardiac troponin C gene. Because MAF1 and MEF-3 are closely related in both recognition sequence and distribution, MAF1 and MEF-3 probably represent the same nuclear factor which may play an important role in muscle gene transcription. Thus, the muscle-specific induction of the aldolase A gene is governed by muscle-specific MEF-2 and existing MEF-3 (MAF1).

The MEF-3 motif is required for MEF-2-mediated skeletal muscle-specific induction of the rat aldolase A gene

The rat aldolase A gene contains two alternative promoters and two alternative first exons. The distal promoter M is expressed at a high level only in skeletal muscle. Previous in vitro transfection studies identified the region from -202 to -85 as an enhancer that is responsible for dramatic activation during the differentiation of chicken primary myoblasts. This enhancer contains an A/T-rich sequence resembling the MEF-2 motif, which is an important element of muscle enhancers and promoters. In this study, we demonstrate that the MEF-2 sequence is essential but not sufficient for the activity of the enhancer. Another region required for the activity was recognized by a nuclear factor, tentatively named MAF1. MAF1 was found in both muscle cells and nonmuscle cells, and MAF1 from both cell types was indistinguishable by gel retardation and DNase I footprint experiments. The sequence required for MAF1 binding is very similar to the MEF-3 motif, which is an element of the skeletal muscle-specific enhancer of the cardiac troponin C gene. Because MAF1 and MEF-3 are closely related in both recognition sequence and distribution, MAF1 and MEF-3 probably represent the same nuclear factor which may play an important role in muscle gene transcription. Thus, the muscle-specific induction of the aldolase A gene is governed by muscle-specific MEF-2 and existing MEF-3 (MAF1).

Chloroplast and cytoplasmic enzymes: isolation and sequencing of cDNAs coding for two distinct pea chloroplast aldolases

Two cDNAs which correspond to two very similar Class I aldolases have been isolated from a pea (Pisum sativum L.) cDNA library. With the exception of one codon they match the experimentally determined N-terminal sequence of a pea chloroplast aldolase. The deduced C-terminal sequence of one of these clones is unique among Class I aldolases. The deduced C-terminus of the other is more like the C-terminus of other eucaryotic Class I aldolases. Comparisons of sequence homology suggest that the pea chloroplast isozymes are only marginally more closely related to the anaerobically induced plant aldolases than to aldolases from animals.

Alternate use of divergent forms of an ancient exon in the fructose-1,6-bisphosphate aldolase gene of Drosophila melanogaster

The fructose-1,6-bisphosphate aldolase gene of Drosophila melanogaster contains three divergent copies of an evolutionarily conserved 3' exon. Two mRNAs encoding aldolase contain three exons and differ only in the poly(A) site. The first exon is small and noncoding. The second encodes the first 332 amino acids, which form the catalytic domain, and is homologous to exons 2 through 8 of vertebrates. The third exon encodes the last 29 amino acids, thought to control substrate specificity, and is homologous to vertebrate exon 9. A third mRNA substitutes a different 3' exon (4a) for exon 3 and encodes a protein very similar to aldolase. A fourth mRNA begins at a different promoter and shares the second exon with the aldolase messages. However, two exons, 3a and 4a, together substitute for exon 3. Like exon 4a, exon 3a is homologous to terminal aldolase exons. The exon 3a-4a junction is such that exon 4a would be translated in a frame different from that which would produce a protein with similarity to aldolase. The putative proteins encoded by the third and fourth mRNAs are likely to be aldolases with altered substrate specificities, illustrating alternate use of duplicated and diverged exons as an evolutionary mechanism for adaptation of enzymatic activities.

Alternate use of divergent forms of an ancient exon in the fructose-1,6-bisphosphate aldolase gene of Drosophila melanogaster

The fructose-1,6-bisphosphate aldolase gene of Drosophila melanogaster contains three divergent copies of an evolutionarily conserved 3' exon. Two mRNAs encoding aldolase contain three exons and differ only in the poly(A) site. The first exon is small and noncoding. The second encodes the first 332 amino acids, which form the catalytic domain, and is homologous to exons 2 through 8 of vertebrates. The third exon encodes the last 29 amino acids, thought to control substrate specificity, and is homologous to vertebrate exon 9. A third mRNA substitutes a different 3' exon (4a) for exon 3 and encodes a protein very similar to aldolase. A fourth mRNA begins at a different promoter and shares the second exon with the aldolase messages. However, two exons, 3a and 4a, together substitute for exon 3. Like exon 4a, exon 3a is homologous to terminal aldolase exons. The exon 3a-4a junction is such that exon 4a would be translated in a frame different from that which would produce a protein with similarity to aldolase. The putative proteins encoded by the third and fourth mRNAs are likely to be aldolases with altered substrate specificities, illustrating alternate use of duplicated and diverged exons as an evolutionary mechanism for adaptation of enzymatic activities.

Autonomous activity of the alternate aldolase A muscle promoter is maintained by a sequestering mechanism

The mouse aldolase A gene contains two closely-spaced alternate promoter/first exons. The more distal of the two, the M promoter, is muscle-specific while the 3' promoter, the H promoter, is expressed constitutively. Various segments from these promoter regions were linked to a reporter gene and used to transfect the myogenic cell line C2C12 and the hepatoma cell line BWTG3. A muscle-specific enhancer, MEN1, responsible for 80% of promoter M activity and containing 4 consensus MyoD binding sites was localized between -2578 to -2723 of the M promoter. Another muscle-specific enhancer and a restrictive element, MEN2/MSE, were found in the interval -1100 to -350. The MSE restrictive element was found to prohibit inappropriate up-regulation of the M promoter by selectively sequestering it from H promoter elements in both myoblasts and myotubes. Among the H promoter elements was found an enhancer, HEN, situated between -533 and -200 which did not function in myotubes. These studies also show that H promoter elements can act synergistically with a non-specific element, MAE, located between -350 and -130 of the M cap site greatly stimulating M promoter transcription in all cell types when the MSE restrictive element was absent. Through the analysis of interactions between these elements and the aldolase A and HSV-TK promoters we showed that neither the enhancers nor the promoter proximal sequences by themselves contain adequate information to reproduce the native pattern of aldolase A promoter modulation. Rather, the sequestering of the M promoter by the MSE restrictive element and the relative positioning and context of promoters M and H appear critical to the regulated expression of aldolase A.

Differential expression of two distinct forms of mRNA encoding members of a dipeptidyl aminopeptidase family

We have identified two cDNAs encoding dipeptidyl aminopeptidase-like proteins (DPPXs) in both bovine and rat brains that have different N-terminal cytoplasmic domains but share an identical transmembrane domain and a long C-terminal extracellular domain. In both species, one of the cDNAs encodes a protein (designated DPPX-S) of 803 amino acid residues with a short cytoplasmic domain of 32 amino acids, and the other cDNA encodes a protein (designated DPPX-L) with a longer cytoplasmic domain--the bovine cDNA encodes 92 amino acids and the rat cDNA encodes 88 amino acids. The membrane topology of DPPX-S and -L is similar to that of other transmembrane peptidases, and DPPX-S share approximately 30% identity and 50% similarity with reported yeast and rat liver dipeptidyl aminopeptidase amino acid sequences, suggesting that DPPX is a member of the dipeptidyl aminopeptidase family. DPPX-S mRNA is expressed in brain and some peripheral tissues including kidney, ovary, and testis; in contrast, DPPX-L mRNA is expressed almost exclusively in brain. No transcripts for either form are found in heart, liver, or spleen. In situ hybridization studies show that the two transcripts have different distributions in the brain. DPPX-L mRNA is expressed in limited regions of brain with the highest level of expression in the medial habenula. More widespread expression is seen for DPPX-S mRNA. The differential distribution of mRNAs for the DPPX-S and -L suggests that these proteins are involved in the metabolism of certain localized peptides and that the cytoplasmic domain may play a key role in determining the physiological specificity of DPPX.

Analysis of upstream regulatory regions required for the activities of two promoters of the rat aldolase A gene

Rat aldolase A gene has 2 promoters with different tissue specificities (M- and AH promoters). The M promoter is active only in adult skeletal muscle and induced during myogenesis, whereas the AH promoter is active ubiquitously in many tissues, including various cancer cells. Regulatory sequences for these promoters were investigated through assays for transient expression after introduction into myogenic and nonmyogenic cells. When M promoter-CAT fusion genes were transfected into primary cultures of chicken myoblasts, expression of CAT activity was drastically induced during myotube formation. The region comprising 202 to 85 base pairs (bp) upstream from the transcription initiation site was found to be necessary for the induction and an enhancer activity whose region includes the AT-rich recognition sequence (MEF-2 binding site). On the other hand, 2 upstream regions were found to be responsible for AH promoter activity expressed in HepG2 cells. The distal region (-280 to -260) of the promoter includes the AP1 binding sequence, whereas the proximal region (-207 to -180) contains a novel inverted repeat consisting of 22 bp but does not contain known promoter and enhancer sequences.

Regulation of the multiple promoters of the human aldolase A gene: response of its two ubiquitous promoters to agents promoting cell proliferation

The human aldolase A gene is transcribed from three distinct promoters, the two ubiquitous promoters PN and PH and the muscle specific promoter PM. In the present study, we investigate further aldolase A mRNA structure and expression. We demonstrate that the upstream N-type exon is, in fact, extremely heterogeneous. RNAse H mapping experiments permit quantification of relative abundance of N, M, and H type mRNAs and show that the level of transcripts containing the downstream H-type exon is at least 30 times higher than that of those containing N exon, in all tissues tested. Aldolase A level is up-regulated in proliferating cells. Here we show that both N and H type mRNAs, although barely detectable in normal liver, are highly expressed in human hepatomas biopsies. Furthermore, in human lymphocytes, N-type mRNA level is enhanced by serum treatment, while in cultured Hep G2 cells, both N-type and H-type mRNA levels are increased by serum and by the tumor promoting agent PMA. Using CAT constructs in transfection experiments, we demonstrate that the H exon plus its upstream region can function autonomously: the 420 base pairs upstream of the H exon are sufficient to confer to promoter PH an efficiency comparable that of the complete SV40 early promoter and enhancer in two cell lines.

An additional promoter functions in the human aldolase A gene, but not in rat

The aldolase A gene was isolated from a human DNA library, mapped and sequenced. This gene comprises 12 exons and spans 6.5 kb. From the genomic DNA sequence and from the previous sequence analysis of the cDNA, it was revealed that the first exon L1 and the second exon encode the 5' non-coding sequence of mRNA L1, while the third and forth exons (corresponding to exons M and L2) encode different mRNA, mRNA M and L2, respectively; the following eight exons (exons 5-12) are shared commonly by all the mRNA species. These results indicate that the mRNA species are generated from a single aldolase A gene from one of exons L1, M or L2, in addition to exons 5-12, and also that the usage of a leader exon is similar but clearly distinct from that of rat aldolase A gene which we analyzed [Joh, K., Arai, Y., Mukai, T. & Hori, K. (1986) J. Mol. Biol. 190, 401-410]. By comparing the promoter regions in the human and rat aldolase A genes, we found similar sequences in the rat genome corresponding to those of the human L1, M and L2 promoter. We could not, however, detect any transcripts starting from sequences corresponding to the human L1 promoter in the rat genome, although the products corresponding to human M and L2 were detected. Thus, we conclude that the L1 promoter was either acquired by the human genome or deleted from the rat genome after human and rat diverged during evolution.

The structure of the brain-specific rat aldolase C gene and its regional expression

The rat aldolase C gene was isolated from a rat genomic DNA library. This gene comprises 9 exons and spans 3590 base pairs. A single copy of the gene occurs per haploid rat genome. The initiation of transcription occurs at two different sites. The cellular localization of aldolase C mRNA was determined in the central nervous system along with aldolase A mRNA by in situ hybridization. The result indicates the predominant expression of this gene in Purkinje cells of the cerebellar cortex, where aldolase A mRNA was rather repressed.

Aldolase DNA polymorphism in subterranean mole-rats: genetic differentiation and environmental correlates

We analysed the genetic diversity and environmental correlates of the aldolase A and B genes by means of restriction endonucleases (DNA RFLP analysis), in the four chromosomal species (2n = 52, 54, 58 and 60) of the actively speciating subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel. The results indicated that: (i) both aldolase genes are highly polymorphic; (ii) fragment frequencies and fragment profiles display geographical patterns and significant ecological correlates; (iii) discriminant analysis largely succeeded in separating the four chromosomal species on the basis of variation of aldolase RFLPs.

Transcriptional regulation of an aldolase gene in the regenerating rat liver

The relative abundance of rat aldolase A, B, C, alpha-fetoprotein, and albumin mRNAs was determined by Northern hybridization during liver regeneration after partial hepatectomy. Aldolase A mRNA increased more than 10-fold on the 3rd day after partial resection compared with that of normal adult rat liver. S1 analysis revealed that three species of aldolase A mRNAs (mRNA I, II & III) reappeared. However, transcriptional rate of aldolase A mRNA did not change at all during the regeneration. In contrast, aldolase B, aldolase C and albumin mRNAs did not change at all. These findings suggest that the differentiated hepatocyte maintains a differentiated state during the liver regeneration as seen in aldolase B, whereas "oncofetal" isozymes such as aldolase A resurge after partial hepatectomy under the control of post-transcriptional mechanism.

Testis-specific transcription initiation sites of rat farnesyl pyrophosphate synthetase mRNA

A variety of rat tissues were screened at low stringency with a rat farnesyl pyrophosphate (FPP) synthetase cDNA. In testis, an FPP synthetase-related RNA was detected that was larger than the liver FPP synthetase mRNA and was present at very high levels comparable with liver FPP synthetase RNA levels obtained from rats fed diets supplemented with cholestyramine and mevinolin. Sequence analysis of testis cDNA clones, together with primer extension and S1 nuclease experiments, indicated that testis FPP synthetase transcripts contain an extended 5' untranslated region. The 5' extension contained one or two out-of-frame upstream ATGs, depending on the site of transcription initiation. Protein in vitro translation studies indicated that the extended 5' untranslated region may play a role in regulating the translation of the FPP synthetase polypeptide in rat testis. Southern blot analysis with a probe containing both testis and liver 5' untranslated sequences provided evidence that both liver and testis transcripts derive from the same gene. The data suggest that an upstream testis-specific promoter results in the abundant production of FPP synthetase transcripts that are translated at low efficiency; another promoter functions in liver and other somatic tissues and directs the regulated synthesis of shorter discrete transcripts.

Testis-specific transcription initiation sites of rat farnesyl pyrophosphate synthetase mRNA

A variety of rat tissues were screened at low stringency with a rat farnesyl pyrophosphate (FPP) synthetase cDNA. In testis, an FPP synthetase-related RNA was detected that was larger than the liver FPP synthetase mRNA and was present at very high levels comparable with liver FPP synthetase RNA levels obtained from rats fed diets supplemented with cholestyramine and mevinolin. Sequence analysis of testis cDNA clones, together with primer extension and S1 nuclease experiments, indicated that testis FPP synthetase transcripts contain an extended 5' untranslated region. The 5' extension contained one or two out-of-frame upstream ATGs, depending on the site of transcription initiation. Protein in vitro translation studies indicated that the extended 5' untranslated region may play a role in regulating the translation of the FPP synthetase polypeptide in rat testis. Southern blot analysis with a probe containing both testis and liver 5' untranslated sequences provided evidence that both liver and testis transcripts derive from the same gene. The data suggest that an upstream testis-specific promoter results in the abundant production of FPP synthetase transcripts that are translated at low efficiency; another promoter functions in liver and other somatic tissues and directs the regulated synthesis of shorter discrete transcripts.

Evidence for alternative RNA splicing and possible alternative promoters in the human muscle phosphofructokinase gene at the 5' untranslated region

Three mRNA species for human muscle phophofructokinase containing heterogeneous 5' untranslated sequences were identified through cDNA cloning. Type A mRNA was essentially the same as that reported previously (Nakajima, H., et al. (1987) FEBS Lett. 223, 113). Type B mRNA was considered to be the major gene product, which contained an extra non-coding sequence within the 5' untranslated region of type A mRNA. Amplification of mRNA by polymerase chain reaction revealed that types A and B mRNAs shared a common precursor RNA, and were alternatively spliced. Type C mRNA, homologous to the cDNA sequence from a placenta library (Sharma, P. M. et al., (1989) Gene 77, 177), was considered to be under the control of an alternative promotor.

A functional splice site in the 5' untranslated region of a zein gene

Zein genes, the genes coding for the zein storage proteins of maize, have a unique gene structure where at least two promoters lie upstream of the coding region. Between the P1 promoter (900 base pairs upstream of the coding region) and the translation initiation AUG codon are 18 short reading frames. A discrepancy between the signals obtained by S1-mapping and primer extension and the DNA sequence in the region of one of these signals suggests the presence of a 3' splice site lying 40 nucleotides upstream of the coding region. A splicing event removing all of the short reading frames from the mRNA transcribed from the P1 promoter would bring this mRNA into a translatable form. Further evidence for a functional 3' splice site has been obtained from sequencing of primer extension products and in vitro splicing of a hybrid intron in the HeLa cell in vitro splicing system.

In vivo activity of the most proximal promoter of the human aldolase A gene and analysis of transcriptional control elements

The genomic region upstream from exon F (exon IV) of the human aldolase A gene has been studied for its ability to direct the transcription of a reporter gene in vivo. Transfection experiments in human hepatoma cells (Hep 3B) followed by CAT assay, and S1 mapping analysis, demonstrated that: (i) this region is able to drive CAT gene transcription; (ii) all the transcriptional control elements of this promoter are downstream from nucleotide -384 of the longer ubiquitous RNA start site and the sequences between -384 and -262 play a crucial role in transcriptional efficiency; (iii) initiation starting points for two mRNAs exist 61 bp apart. Gel retardation and footprinting assays demonstrated the presence of DNA-protein complexes mainly in the region between -384 and -262 and such ubiquitous binding factors as Sp1 and AP-1.

The brain-specific gene for rat aldolase C possesses an unusual housekeeping-type promoter

A DNA fragment encompassing the first exon and about 750 bp of the 5'-flanking sequence has been isolated and sequenced. The gene has multiple start sites of transcription which are dispersed over about 200 bp. The promoter lacks TATA and CAAT boxes and is very G + C-rich, with putative binding sites for the transcriptional factors Sp1 and AP2. Similar features are shared with two other brain-specific genes encoding thy-1 antigen and gamma-enolase. The existence of a conserved block of similarity upstream of the human and rat aldolase C genes suggests that this region could be involved in tissue-specific expression whose mechanism seem to be, at least in part, transcriptional.

Construction and expression of human aldolase A and B expression plasmids in Escherichia coli host

E. coli expression plasmids for human aldolases A and B (EC 4.1.2.13) have been constructed from the pIN-III expression vector and their cDNAs, and expressed in E. coli strain JM83. Enzymatically active forms of human aldolase have been generated in the cells when transfected with either pHAA47, a human aldolase A expression plasmid, or pHAB 141, a human aldolase B expression plasmid. These enzymes are indistinguishable from authentic enzymes with respect to molecular size, amino acid sequences at the NH2- and COOH-terminal regions, the Km for substrate, fructose 1,6-bisphosphate and the activity ratio of fructose 1,6-bisphosphate/fructose 1-phosphate (FDP/F1P), although net electric charge and the Km for FDP of synthetic aldolase B differed from those for a previously reported human liver aldolase B. In addition, both the expressed aldolases A and B complement the temperature-sensitive phenotype of the aldolase mutant of E. coli h8. These data argue that the expressed aldolases are structurally and functionally similar to the authentic human aldolases, and would provide a system for analysis of the structure-function relationship of human aldolases A and B.

Transcription of rat aldolase B gene: minor RNAs are transcribed by RNA polymerase III

Rat aldolase B gene was confirmed to have multiple transcriptional initiation sites; one site for the major transcript and at least two sites for the minor transcripts which are located at about 30 to 60 bases upstream of the major site. Although the transcription of the minor transcripts was entirely resistant to 1 microgram/ml of alpha-amanitin, which inhibits RNA polymerase II, it was completely blocked by 1000 micrograms/ml of the drug which inhibits RNA polymerase III. The box A- and B-like sequences, which are known to exist in the internal split promoter region of class III genes, were also found to be located around the initiation sites of two minor transcripts from the rat aldolase B gene. Analyses using deletion mutants of the promoter region of the gene suggested that the synthesis of the minor transcripts depends on the box A- and B-like sequences, but does not depend on a TATA promoter element. Northern blot analysis indicated that the minor transcripts are only a few percent of the total transcripts derived from the aldolase B gene. Some of the minor transcripts analyzed were shown to have a mature size in the poly(A)+ RNA fraction. Thus, the minor transcripts of rat aldolase B gene are apparently transcribed by RNA polymerase III, and subsequently normally processed and polyadenylated. The possible function of these minor transcripts will be discussed.

Alternative promoter usage by aldolase A during in vitro myogenesis

Aldolase A in the mouse, as in human and rat, shows tissue-specific variability of message size. In addition, in muscle tissue the mRNA size is also developmentally regulated. In order to determine whether this muscle-specific regulatory mechanism can be reproduced in vitro, we have examined the mRNA species of aldolase A isolated from mouse C2C12 myoblasts and myotubes on Northern blots and by primer extension. We show that aldolase A mRNA increases during in vitro myogenesis; that this induction is accompanied by a change in the message population; and that this change is due to activation of a muscle-specific alternative promoter.

Anaerobically regulated aldolase gene of maize. A chimaeric origin?

The sequence of the anaerobically induced fructose 1,6-bisphosphate aldolase gene of maize is presented. Analysis of the upstream sequences of the aldolase gene reveals a six base-pair sequence (TGGTTT) with perfect homology to one of the sub-regions of the anaerobic regulatory element (ARE) which is responsible for the anaerobic induction of the maize alcohol dehydrogenase 1 gene (Adh1). In the aldolase gene this sequence is located at position -70 relative to the start of transcription, in a small segment proven by functional analysis to be important for expression of the aldolase gene. Since this six base-pair sequence has been shown to be critical for anaerobic induction of the Adh1 mRNA, is in the functional promoter region of aldolase and is also present in a homologous position in Adh2 (another anaerobically-induced gene), we suggest this hexanucleotide is essential for anaerobic regulation of each of these genes. The maize aldolase gene is about 50% homologous at the amino acid level to the animal aldolase gene but has a completely different intron/exon structure. While the rat aldolase gene has nine introns the maize gene has a single large intron near the N terminus of the coding region. Because there is 55% homology downstream from the intron and very little homology upstream, we suggest that the maize gene has acquired a 5' region containing signals for anaerobic regulation and fortuitously adding a new N-terminal region to the protein. We must suppose that the plant gene has lost the remaining introns.

Human aldolase A gene. Structural organization and tissue-specific expression by multiple promoters and alternate mRNA processing

The complete nucleotide sequence of the human aldolase A isoenzyme gene is reported. The cloned gene sequence, spanning 7530 bp, includes twelve exons and occurs as a single copy per haploid human genome. The structural organization of the gene is quite complex: eight exons containing the coding sequence are common to all mRNAs extracted from human and other mammalian sources; four additional exons are present in the 5' untranslated region, of these one is contained in the ubiquitous type of mRNA, the second is in the muscle-specific type of mRNA and the third and fourth are in a minor species of mRNA found in human liver tissue. Furthermore, the determined sequence includes 1000 nucleotides upstream from the first exon (exon I) in the 5' flanking region, and 400 nucleotides, which include the polyadenylation signal, downstream from the termination codon. S1-nuclease-protection analysis of the 5' end of mRNA extracted from human cultured fibroblasts, muscle and hepatoma cell lines indicates the existence of four different transcription-initiation sites. The latter are also supported by the presence of conventional sequences for eukaryotic promoters. Therefore, the four promoters on the same gene generate different tissue-specific transcripts, which share the translated sequence, but each has a unique 5' untranslated region as a result of differential mRNA processing. The nucleotide homology at the coding region and the intron-exon organization of the three human and mammalian aldolase A, B and C genes confirm that they arose from a common ancestral gene, and that aldolase B diverged first.

Transcription of the dystrophin gene in human muscle and non-muscle tissue

The gene that is defective in patients with Duchenne and Becker muscular dystrophy consists of about 60 short exons scattered along a gigantic DNA region that spans some 2 megabase pairs. The encoded protein, dystrophin, was recently characterized as a component of muscle intracellular membranes of low abundance. The dystrophin messenger RNA is difficult to study in both normal and pathological tissue specimens because it is large (14 kilobases) and scarce (0.01-0.001% of total muscle mRNA). We report here that efficient in vitro co-amplifications of the mRNAs of the dystrophin gene and of a reporter gene, aldolase A, by the polymerase chain reaction procedure enables us to obtain a quantitative estimate of the dystrophin gene transcript. A processed, transcribed segment was thus detected in 13 different human tissues. It ranged from 0.02-0.12% of total mRNA in skeletal muscle to 25,000 times less in lymphoblastoid cells.

Isolation of four rat creatine kinase genes and identification of multiple potential promoter sequences within the rat brain creatine kinase promoter region

Rat genes encoding muscle creatine kinase (gene ckm) and brain creatine kinase (gene ckb) have been cloned. The two genes have an identical intron-exon distribution, although introns of the ckb gene are much smaller than those for ckm. The complete nucleotide sequence has been determined for the ckb gene. 5'-Flanking sequences have been compared for both ckm and ckb. The ckb gene has a structurally complex 5'-flanking region with multiple TATA and CAAT sequences suggesting that the gene may contain overlapping promoter elements. Examination of ckb RNA from brain tissue provides no evidence for the existence of more than one set of transcriptional start points. The ckm and ckb genes show little homology in the 5'-flanking regions, although we observed some sequence conservation in the regions immediately surrounding the CAAT and TATA sequences. The rat genome also contains two other creatine kinase-like sequences which may represent processed pseudogenes or mitochondrial creatine kinase.

The structure of brain-specific rat aldolase C mRNA and the evolution of aldolase isozyme genes

The cDNA clones for rat aldolase C mRNA having the nearly complete length were isolated from a rat brain cDNA library and sequenced. The nucleotide sequence of pRAC2-1, a cDNA clone having the largest cDNA insert, indicates that the cDNA is composed of a 105-base-pair 5'-noncoding sequence, a 1089-base-pair coding-sequence and a 382-base-pair 3'-noncoding sequence. The amino acid sequence of aldolase C deduced from a possible open reading frame was composed of 362 residues having a relative molecular mass of 39,164 excluding the initiating methionine, one amino acid shorter than aldolases A and B. The length of aldolase c mRNA was 1750 residues, somewhat longer than that of the aldolase A and B transcripts. The aldolase C mRNA was distributed mainly in the brain, some in ascites hepatoma and fetal liver. Comparison of the amino acid sequences of rat aldolase C with those for rat aldolase A and B [Joh et al. (1985) Gene 39, 17-24; Tsutsumi et al. (1984) J. Biol. Chem. 259, 14572-14575], which have been determined previously, shows the existence of highly conserved stretches of amino acid among the three isozymic forms throughout their sequences. The extent of the homology between aldolases A and C is 81%, while those between aldolases A and B, and B and C are 70%, respectively. The analysis of amino acid substitution among aldolases A, B and C from several species suggests that the isozyme genes diverged much earlier than animal species appeared and that the aldolase C gene has evolved from the aldolase A gene after aldolase A and B genes diverged.