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

Tissue-dependent loss of phosphofructokinase-M in mice with interrupted activity of the distal promoter: impairment in insulin secretion

Phosphofructokinase is a key enzyme of glycolysis that exists as homo- and heterotetramers of three subunit isoforms: muscle, liver, and C type. Mice with a disrupting tag inserted near the distal promoter of the phosphofructokinase-M gene showed tissue-dependent differences in loss of that isoform: 99% in brain and 95-98% in islets, but only 50-75% in skeletal muscle and little if any loss in heart. This correlated with the continued presence of proximal transcripts specifically in muscle tissues. These data strongly support the proposed two-promoter system of the gene, with ubiquitous use of the distal promoter and additional use of the proximal promoter selectively in muscle. Interestingly, the mice were glucose intolerant and had somewhat elevated fasting and fed blood glucose levels; however, they did not have an abnormal insulin tolerance test, consistent with the less pronounced loss of phosphofructokinase-M in muscle. Isolated perifused islets showed about 50% decreased glucose-stimulated insulin secretion and reduced amplitude and regularity of secretory oscillations. Oscillations in cytoplasmic free Ca(2+) and the rise in the ATP/ADP ratio appeared normal. Secretory oscillations still occurred in the presence of diazoxide and high KCl, indicating an oscillation mechanism not requiring dynamic Ca(2+) changes. The results suggest the importance of phosphofructokinase-M for insulin secretion, although glucokinase is the overall rate-limiting glucose sensor. Whether the Ca(2+) oscillations and residual insulin oscillations in this mouse model are due to the residual 2-5% phosphofructokinase-M or to other phosphofructokinase isoforms present in islets or involve another metabolic oscillator remains to be determined.

Alteration of the levels of the M-type 6-phosphofructo-1-kinase mRNA isoforms during neonatal maturation of heart, brain and muscle

During muscle, heart, and brain neonatal maturation, the capacity to utilize glucose in energy metabolism is directly related to the extent of accumulation of the 6-phosphofructo-1-kinase (PFK) M-type subunit. Neonatal development of other organs, such as liver and kidney, which are not characterized by large increases in the capacity to use glucose do not exhibit large increases in the M-type subunit protein. The presence of the M-type subunit in a PFK isozyme pool fosters a higher affinity utilization of carbohydrate and increased responsiveness to the levels of regulatory metabolites. To better appreciate this phenomenon, which is vital for normal development, the different isoforms of the M-type subunit mRNA's and alteration of their levels during maturation have been examined. Further, the potential promoter regions, i.e., the regions upstream from the sites of initiation of transcription, which are involved in expression of the different M-type subunit mRNA isoforms have been isolated, sequenced, and examined for possible transcription factor interaction sites. Using cDNA libraries produced from adult rat brain or skeletal muscle RNA, two primary forms of rat M-type subunit cDNA's were detected. Although the translated regions of these mRNA's were essentially identical, the 5'-untranslated region (5'-UTR) exhibited different lengths (90 or 59 bp) and sequences. Each M-type subunit cDNA had 10 common nucleotides immediately upstream from the initiator ATG, and the remaining 5'-UTR's had insignificant identity. A genomic fragment which interacted with probes complimentary to the sequences of the 5'-UTR of each M-type subunit mRNA isoform was isolated and sequenced by primer walking. It was discovered that the 5'-UTR of one of the mRNA's (proximal mRNA) was located immediately upstream from exon I and was apparently transcribed without splicing. Subsequently, the initial bp in the sequence of the other mRNA isoform (distal mRNA) was located 4010 bp upstream from the ATG in exon 1. Employing Reverse Transcription-Polymerase Chain Reaction using total RNA and scanning densitometry, the relative levels of the proximal and distal mRNA's during neonatal maturation of brain, heart, and muscle were measured. In these tissues, both forms of M-type subunit mRNA's were present, and during maturation tissue-specific differences were noted.

Alteration of 6-phosphofructo-1-kinase subunit protein, synthesis rates, and mRNA during rat neonatal development

For the three 6-phosphofructo-1-kinase (PFK) subunits in heart, skeletal muscle, liver and kidney, developmentally-associated changes in protein, mRNA and apparent synthesis rates were observed. During neonatal maturation, all three phenomena for the M-type in heart and skeletal muscle exhibited large increases. Also, during neonatal development, the L-type and C-type subunits were unaffected in heart but disappeared from skeletal muscle. In the newborn liver and kidney, the amounts of each type of PFK subunit protein were nearly identical. During neonatal development, the levels of all three PFK subunit proteins in kidney increased more than twofold; and this was associated with a similar increase in apparent subunit synthesis rates and mRNA levels. During liver neonatal development, the L-type subunit protein, synthesis and mRNA levels also increased more than twofold. However, during hepatic maturation, M-type subunit protein, synthesis and mRNA levels were unchanged and apparently unaffected. The C-type subunit protein during neonatal liver development decreased approximately 80% as did its apparent synthesis rate. These data suggest that regulation of the alteration of the PFK subunit proteins during neonatal maturation can vary among these tissues and is not the same for each subunit type. Different mechanisms, such as transcription, translation, and mRNA stability could be involved.

Nonsense mutation in the phosphofructokinase muscle subunit gene associated with retention of intron 10 in one of the isolated transcripts in Ashkenazi Jewish patients with Tarui disease

Mutations in the human phosphofructokinase muscle subunit gene (PFKM) are known to cause myopathy classified as glycogenosis type VII (Tarui disease). Previously described molecular defects include base substitutions altering encoded amino acids or resulting in abnormal splicing. We report a mutation resulting in phosphofructokinase deficiency in three patients from an Ashkenazi Jewish family. Using a reverse transcription PCR assay, PFKM subunit transcripts differing by length were detected in skeletal muscle tissue of all three affected subjects. In the longer transcript, an insertion of 252 nucleotides totally homologous to the structure of the 10th intron of the PFKM gene was found separating exon 10 from exon 11. In addition, two single base transitions were identified by direct sequencing: [exon 6; codon 95; CGA (Arg) to TGA (stop)] and [exon 7; codon 172; ACC (Thr) to ACT (Thr)] in either transcript. Single-stranded conformational polymorphism and restriction enzyme analyses confirmed the presence of these point substitutions in genomic DNA and strongly suggested homozygosity for the pathogenic allele. The nonsense mutation at codon 95 appeared solely responsible for the phenotype in these patients, further expanding genetic heterogeneity of Tarui disease. Transcripts with and without intron 10 arising from identical mutant alleles probably resulted from differential pre-mRNA processing and may represent a novel message from the PFKM gene.

Phosphofructokinase deficiency: recent advances in molecular biology

Phosphofructokinase (PFK) plays a major role in glycolysis. Deficiency of PFK-M is characterized by muscle weakness due to fuel crisis in exercising muscles. To elucidate the gene defect of PFK-deficient patients, we have cloned and determined the complete structure and transcription mechanism of human PFK-M mRNA and gene. Molecular defects were investigated in three unrelated Japanese family cases. The first case was characterized by a point mutation at the donor site of intron 15 of the PFK-M gene. Cryptic splicing resulted in a 25 amino acid truncation in the patient's PFK-M. The second case possessed a point mutation at the donor site of intron 19, resulting in the skipping of exon 19 and the truncation of 55 amino acids. In the third case, a missense mutation was identified in the coding region. The review of an updated mutation repertoire indicates the heterogeneity of the molecular mechanism of the disease.

Mutations in muscle phosphofructokinase gene

Mutations in the muscle phosphofructokinase gene (PFK-M) result in a metabolic myopathy characterized by exercise intolerance and compensated hemolysis. PFK deficiency, glycogenosis type VII (Tarui disease) is a rare, autosomal, recessively inherited disorder. Multiple mutations, including splicing defects, frameshifts, and missense mutations, have recently been identified in patients from six different ethnic backgrounds establishing genetic heterogeneity of the disease. There is no obvious correlation between the genotype and phenotypic expression of the disease. PFK-M deficiency appears to be prevalent among people of Ashkenazi Jewish descent. Molecular diagnosis is now feasible for Ashkenazi patients who share two common mutations in the gene; the more frequent is an exon 5 splicing defect, which accounts for approximately 68% of mutant alleles in this population.

Novel clustering of Sp1 transcription factor binding sites at the transcription initiation site of the human muscle phosphofructokinase P1 promoter

The regulatory sequence elements of the human muscle phosphofructokinase (HPFKM) p1 promoter from -655 to +78 were cloned and characterized. In the human cervical carcinoma cell line, HeLa S3, the HPFKM type C RNA initiated from a single predominant transcription initiation site and the HPFKM p1 promoter displayed transcriptional activity in transient transfection assays. The HPFKM p1 promoter region was shown to possess eight binding sites for the Sp1 transcription factor by DNase I footprinting and gel retardation analysis. The functional importance of these interactions was examined by transient transfection analysis in Drosophila SL2 and HeLa S3 cells. This analysis demonstrated that the HPFKM p1 promoter sequence between +12 and +78 retained Sp1-dependent transcriptional activity in Drosophila SL2 cells and retained promoter activity in HeLa S3 cells. These results suggest that the Sp1 binding site (site 8 between +12 and +21) immediately adjacent to the transcription initiation site represents an important regulatory element of this promoter at least in the context of the minimal HPFKM p1 promoter. However mutagenesis of the Sp1 site 8 demonstrated that, in the context of a larger HPFKM p1 promoter region containing Sp1 sites 1 to 7, it now contributed very little to the total promoter activity. Therefore it appears the Sp1 sites in the HPFKM p1 promoter display functional redundancy.

Expression of mouse phosphofructokinase-M gene alternative transcripts: evidence for the conserved two-promoter system

Molecular cloning of the 5' part of mouse phosphofructokinase-M cDNA was performed. In the 46 cDNA clones isolated, there were two classes of 5' untranslated sequences. One had an EcoRI site within its 5' untranslated sequence. This showed 83.0% similarity with human type B mRNA for phosphofructokinase-M. The other lacked an EcoRI site, showing 92.9% similarity with human type C mRNA. Using the reverse-transcription PCR technique, we found that the transcript with an EcoRI site was exclusively expressed in cardiac and skeletal muscles, while that without an EcoRI site was expressed in all the mouse tissues examined. The results suggested that the mouse phosphofructokinase-M gene was transcribed through alternative splicing by the multiple promoters. This transcription mechanism was considered to be evolutionarily conserved. The level of phosphofructokinase-M gene expression in mouse cardiac and skeletal muscles decreased in the ketotic diabetic state. Although the regulatory mechanism and the physiological significance are not fully known, this would indicate that phosphofructokinase-M gene transcripts are affected during the diabetic state.

Regulation of transcription from the human muscle phosphofructokinase P2 promoter by the Sp1 transcription factor

The human muscle phosphofructokinase (HPFKM) p2 promoter contains sequence elements that are similar to the Sp1 transcription factor binding site consensus sequence. DNase I footprinting identified four regions of the HPFKM p2 promoter that bound purified Sp1. Gel retardation analysis using HeLa S3 nuclear extracts and purified Sp1 protein demonstrated that each of the four recognition elements bound the Sp1 transcription factor. The function of the HPFKM p2 promoter elements was examined in transient transfection assays using these binding sites cloned into a minimal promoter element. In Drosophila Schneider line-2 cells, each of these regulatory regions trans-activated transcription from a minimal promoter element in response to exogenously expressed Sp1. In addition, transcription from the HPFKM p2 promoter was shown to be trans-activated by exogenously expressed Sp1 in Drosophila Schneider line-2 cells. Deletion analysis of the HPFKM p2 promoter demonstrated that the promoter region between -66 and +16 was sufficient to confer sp1 responsiveness. This promoter region includes one of the regulatory elements footprinted by the purified Sp1 transcription factor and mediates the majority of the transcriptional activity from the HPFKM p2 promoter in the human cervical carcinoma cell line HeLa S3. This demonstrates that the HPFKM p2 promoter contains four functional Sp1 binding sites that may contribute to the level of transcription from this promoter in a variety of cell types.

Control of the murine phosphofructokinase-A gene during muscle differentiation

The muscle-specific isoform of phosphofructokinase (PFK-A) is induced during muscle development. To understand expression of PFK at the molecular level, transcription of the mouse PFK-A gene was examined during C2 myoblast differentiation to myotubes. PFK-A gene transcription increased 5-7-fold during differentiation in vitro. To identify cis-acting elements which direct muscle-specific transcription of the PFK-A gene, its 5'-flanking region and first exon were cloned and characterized. S1 nuclease protection and primer extension assays showed four sites of transcription initiation at 106, 105, 88, and 87 bp upstream of the translation initiation codon. Stable transfection of fusion genes linking -1900 to +99 of PFK-A 5'-flanking sequence to chloramphenicol acetyltransferase coding sequences into myogenic C2 cells did not confer muscle-specific expression. However, larger fragments of PFK-A 5'-flanking region (-5800 to +99) showed muscle-specific expression by transient transfection assay. The sequences directing muscle-specific transcription were further defined by linking various PFK-A upstream fragments to the luciferase gene under the control of the PFK-A proximal promoter, -335 to +99 bp. We found DNA sequence responsible for muscle-specific expression of the PFK-A gene between -4800 and -3900 bp.

Cloning and characterization of the human muscle phosphofructokinase gene

A 35-kbp region of genomic DNA encoding the human muscle phosphofructokinase (HPFK-M) gene including all of the coding exons (1-22) plus 2.2-kbp of 5'-flanking sequence has been cloned. The exon boundaries are the same as has been observed for the rabbit muscle phosphofructokinase (RPFK-M), the human liver phosphofructokinase (HPFK-L), and the mouse liver phosphofructokinase (MPFK-L) genes. Characterization of the structure of the HPFK-M gene and its transcript in Epstein-Barr virus transformed B-cell lines derived from patients with glycogen storage disease type VII (GSDVII or Tarui's disease) demonstrated that this single-copy gene encodes a normal sized 3.0-kb transcript in the four cases examined. This suggests the lesion in these cases represents either a point mutation or possibly a small insertion or deletion resulting in the synthesis of a defective HPFK-M protein. Analysis of the 5'-flanking region demonstrated the presence of a functional promoter located within 114 nucleotides of a proposed transcription initiation site. This promoter was active in the human cervical carcinoma cell line, HeLa S3, the dedifferentiated human hepatoma cell line, HepG2.1, and the mouse myoblast cell line, C2C12, suggesting this promoter has a broad cell-type specificity. In addition, from the known HPFK-M cDNA sequences, this observation indicates that the HPFK-M gene has a second promoter located upstream from the genomic region isolated in this study.

Metabolic control of gene expression: in vivo studies with transgenic mice

Transgenic animals provide a comprehensive model for investigating genes encoding inducible enzymes involved in metabolism, since the molecular mechanisms regulating gene transcription can be studied in the whole animal. Studies on the promoters of the genes encoding two key enzymes in the gluconeogenic and glycolytic pathways--phosphoenol-pyruvate carboxykinase and pyruvate kinase are described as examples of this approach. Work on the phosphoenolpyruvate carboxykinase promoter using transgenic mice has been particularly informative: the cis-acting elements involved in hormonal regulation, tissue specificity and developmental inhibition of gene expression have been identified and their function in vivo examined.

Rat-liver-type phosphofructokinase mRNA. Structure, tissue distribution and regulation

We have cloned a full-length cDNA for rat-liver-type phosphofructokinase. The similarities of the rat liver-type phosphofructokinase mRNA to the human and mouse counterparts were 94% and 99% in their amino acid sequences and 88% and 94% in the nucleotide sequences of their coding regions, respectively. Rat liver-type phosphofructokinase mRNA was expressed in all tissues examined, but its level was regulated tissue-specifically. The nutritional and hormonal regulations of the mRNA in the liver were examined in comparison with those of two other key glycolytic enzymes, glucokinase and L-type pyruvate kinase. The level of liver-type phosphofructokinase mRNA was essentially unchanged by starvation (72 h) or diabetes. The mRNA level also did not change significantly on refeeding starved rats on a high carbohydrate diet, or treating diabetic ones with insulin. These results suggested that rat liver-type phosphofructokinase mRNA in the liver was not under control of diet or insulin, in contrast to glucokinase and L-type pyruvate kinase.

Complex pattern of alternative splicing generates unusual diversity in the leader sequence of the chicken link protein mRNA

We report here the isolation of the 5' end and the promoter region of the gene for chicken cartilage link protein, and demonstrate extensive heterogeneity of the leader sequence arising from differential utilization of multiple splice sites within the 5'-most exon. The 500-base pairs (bp) exon 1 consists of solely untranslated sequence and is followed by an intron greater than 33 kilobase pairs (kb). Together, the five exons predict a gene size longer than 100 kb. Multiple transcription initiation sites were mapped 34, 46, 56, 66 and 76 bp downstream of a TATA-like motif. Sequence analysis revealed that in addition to the non-spliced variant, multiple mRNA species were generated by alternative splicing resulting in the exclusion of 92, 166, 170, 174 and 263 nucleotides (nt), respectively, from exon 1. Polymerase chain reaction confirmed the existence of various splice forms, and showed cell type- and developmental stage-specific expression for one group of them. Secondary structure predictions indicated that the leaders of the splice forms could form stable hairpin structures with different free energies of formation (up to delta G = -110 kcal/mol), suggesting translational control. The splice variant detected in the largest amount had the least stable predicted hairpin (delta G = -31.7 kcal/mol).

Structure of the entire human muscle phosphofructokinase-encoding gene: a two-promoter system

We have recently shown that three types (A,B, and C) of mRNA species are transcribed from a single gene encoding human muscle phosphofructokinase (hPFK-M) through alternative splicing [Nakajima et al., Biochem. Biophys. Res. Commun. 166 (1990) 637-641]. To determine its complete structure and elucidate the mechanism of alternative RNA splicing, we isolated the hPFK-M gene, which spans about 30 kb, and contains 24 exons. Transcription start points were observed for both exon 1 and exon 2 by S1 nuclease protection assay and primer extension. Motifs of an Sp1-binding site were observed in the upstream region of exon 1 (promoter 1). A TATA-box-like sequence and a CAAT-box-like sequence were identified in the upstream region of exon 2 (promoter 2). Reporter assay revealed that the promoter 1 region was functional both in HeLa cells and myoblastic clonal cells, and that the promoter 2 region was active only in myoblastic cells. Motifs of M-CAT known as a muscle-specific enhancer, were observed in the promoter 2 region. These results indicated that the hPFK-M gene contains at least two promoter regions, facilitating the expression of the heterogeneous gene transcripts in a cell-type-specific manner.

Tissue-specific and dexamethasone-inducible expression of alkaline phosphatase from alternative promoters of the rat bone/liver/kidney/placenta gene

The rat Bone/Liver/kidney/Placenta Alkaline Phosphatase (ALP) is transcribed from two alternative promoters spaced over 25 kb apart, resulting in two variant transcripts that are identical in their coding sequence. We investigated the steady-state levels of the two variant transcripts in various rat tissues and cell lines using the polymerase chain reaction (PCR) amplification for RNA phenotyping, RNase protection, and northern blot analysis. Our results demonstrate that ALP transcripts from the upstream promoter are preferentially expressed in calvariae, and are almost exclusively expressed in ROS17/2.8 osteogenic sarcoma cells. In contrast, the downstream promoter is preferentially expressed in kidney. Moreover, the increase in ALP activity and mRNA levels following dexamethasone treatment of ROS17/2.8 cells is correlated with an increase in the level of transcripts from the upstream promoter. Thus, the two alternative promoters of the rat BLKP ALP gene are involved in cell-specific and dexamethasone-inducible regulation of its expression.

Tissue specificity in expression and alternative RNA splicing of human phosphofructokinase-M and -L genes

Mode of the expression of phosphofructokinase (PFK) -M and -L genes was examined in various human tissues including muscle, placenta, liver, kidney, pancreas, stomach and reticulocytes. The gross level of mRNA expression of PFK-M and -L genes was estimated by Northern analysis. Polymerase chain reaction was used to detect mRNA expressed at low levels in these tissues. Tissue-specific expression of alternatively spliced PFK-M gene transcripts was also determined by polymerase chain reaction. The results indicated that alternative splicing of PFK-M gene transcripts was controlled in a tissue-specific manner.

Sequence diversity in the 5' untranslated region of rabbit muscle phosphofructokinase mRNA

DNA sequences of two full-length rabbit muscle phosphofructokinase (RMPFK) cDNAs (A and B) show identical coding sequence but heterogeneous 5' untranslated regions. cDNA-A is formed by removal of a 1.7 kb upstream intron while cDNA-B retains the 3' region of this intron. A 2.8 kb upstream sequence of RMPFK gene contains several features characteristic of housekeeping genes: high GC content (67%) at its 5' end, with 50 CpG sites; five Sp1 sites; and no functional TATA box. Comparison of the 5' sequences of the two RMPFK cDNAs and three human muscle PFK cDNAs (Nakajima, H., et al., (1990) Biochem. Biophys. Res. Com. 166, 637) suggests that a single splicing event occurs involving different splicing donor sites but the same splicing acceptor site, resulting in diversity in the upstream sequence. These observations suggest that transcription of muscle PFK gene may start at multiple sites, another feature of housekeeping genes.