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PubMed2000

Circadian rhythms of sterol 12alpha-hydroxylase, cholesterol 7alpha-hydroxylase and DBP involved in rat cholesterol catabolism.

Circadian rhythms of important enzymes involved in the conversion of cholesterol to bile acids [sterol 12alpha-hydroxylase (12alpha-hydroxylase) and cholesterol 7alpha-hydroxylase (7alpha-hydroxylase)] and an albumin site D-binding protein (DBP) were examined in rats. When the animals were fed freely, they usually ate in the dark and the circadian rhythms of activities of 12alpha-hydroxylase and 7alpha-hydroxylase showed the same peaks (at 10 p.m.) and lows (at 2 p.m.). Their mRNA levels were determined at four timepoints: 3 a.m., 10 a.m., 3 p.m. and 10 p.m. A maximum of the rhythm of 12alpha-hydroxylase was observed at 3 p.m. and the minimum at 3 a.m. These results are distinct from those of 7alpha-hydroxylase, whose maximum point was at 10 p.m. and minimum at 3 p.m. When the rats were fed only in the day-time (from 9 a.m. to 5 p.m.), a marked shift of the activity and mRNA rhythms was observed with both enzymes. The circadian rhythms of the activities of both enzymes showed the same peaks (at 3 p.m.), but the mRNA levels of 12alpha-hydroxylase were distinct from those of 7alpha-hydroxylase, whose maximum point was at 3 a.m. and minimum at 10 p.m. Differences between the maximum and the minimum points of each enzyme mRNA level were statistically significant (P < 0.01 for 12alpha-hydroxylase and 0.05 for 7alpha-hydroxylase). Moreover, circadian rhythms of DBP were also markedly shifted with the change of feeding period. The maximum mRNA level was observed at 10 p.m. instead of 10 a.m. and the minimum was at 10 a.m. instead of 10 p.m.

Animals↗
PubMed2026

DBP-CanPred: a machine learning model for predicting cancer-causing mutations in DNA-binding proteins.

INTRODUCTION: The fundamental cellular processes, including transcriptional regulation, chromatin organization, and genome maintenance, are regulated by DNA-binding proteins (DBPs). Mutations in DBPs can alter protein-DNA interactions, leading to tumor development. However, identifying such driver mutations remains a major challenge due to limitations of experimental approaches. METHODS: We have trained a machine learning model, DBP-CanPred, to identify driver mutations in DBPs. We used the sequence-derived evolutionary features, as well as structure-based features such as mutation-perturbed structural descriptors. RESULTS: We evaluated DBP-CanPred using a curated test set, achieving an AU-ROC of 0.86 and a balanced accuracy of 0.79. Further analysis based on substitution-type showed consistent performance across different categories, especially higher performance on charged residues. In addition, we applied the model on an independent dataset and identified potential driver mutations with high confidence scores. DISCUSSION: The study contributes to understanding mutation patterns in DNA-binding proteins and supports variant interpretation in cancer research.

DNA-binding proteins↗
PubMed1998

Evolutionarily conserved, "acatalytic" carbonic anhydrase-related protein XI contains a sequence motif present in the neuropeptide sauvagine: the human CA-RP XI gene (CA11) is embedded between the secretor gene cluster and the DBP gene at 19q13.3.

Conserved amino acid motifs are found in numerous expressed genes. Proteins and peptides with functional relationships may be identified using probes designed to hybridize with these motifs. An oligonucleotide probe was prepared to match the sequence of the expected active region of a frog corticotropin-releasing factor-like peptide sauvagine and used to screen a sheep brain cDNA library. A novel 1331-bp cDNA encoding a putative 328-residue protein with a theoretical mass of 36 kDa was identified. The presence of a strong signal sequence indicates that it is a secreted protein. The amino- and carboxy-terminal regions are characterized by several potential phosphorylation sites and binding motifs, suggesting a role in intracellular signal transduction. Although the protein possesses a 7-residue sequence identical to that found in sauvagine, its overall primary structure most closely resembles those of the alpha-carbonic anhydrases (alpha-CAs). Moreover, the detection of the human and mouse orthologues in the EST databases, together with an evolutionary analysis, indicates that the protein represents a new member of the alpha-CA gene family, which we designate carbonic anhydrase-related protein XI (CA-RP XI), encoded by CA11 (human) and Car11 (mouse, rat). The human CA11 gene appears to be located between the secretor type alpha(1,2)-fucosyltransferase gene cluster (FUT1-FUT2-FUT2P) and the D-site binding protein gene (DBP) on chromosome 19q13.3. Despite potentially inactivating changes in the active-site residues, CA-RP XI is evolving very slowly in mammals, a property indicative of an important function, which has also been observed in the two other "acatalytic" CA isoforms, CA-RP VIII and CA-RP X, whose functions are unknown.

Amino Acid Sequence↗
PubMed1995

Developmental patterns of diurnal variations in 3-hydroxy-3-methylglutaryl coenzyme A reductase, D-site binding protein (DBP), and serine dehydratase mRNA levels in rat liver.

Rats were housed under a 12-hr light (07:00-19:00)/12-hr dark cycle. Hepatic 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA appeared at 3 weeks of age, and diurnal variation was established at 5 weeks of age. Diurnal variation of the D-Site binding protein (DBP) mRNA was faintly seen 1 week after birth and became evident with age. Serine dehydratase mRNA level was high at 11:00 in the livers of rats at 2-3 days of age, and at 15:00 in those at 1-2 weeks of age. The rhythm became ambiguous at 3-4 weeks of age, but an adult-type rhythm with a peak at 19:00 was established at 5 weeks of age.

Animals↗
PubMed2006

The circadian PAR-domain basic leucine zipper transcription factors DBP, TEF, and HLF modulate basal and inducible xenobiotic detoxification.

The PAR-domain basic leucine zipper (PAR bZip) transcription factors DBP, TEF, and HLF accumulate in a highly circadian manner in several peripheral tissues, including liver and kidney. Mice devoid of all three of these proteins are born at expected Mendelian ratios, but are epilepsy prone, age at an accelerated rate, and die prematurely. In the hope of identifying PAR bZip target genes whose altered expression might contribute to the high morbidity and mortality of PAR bZip triple knockout mice, we compared the liver and kidney transcriptomes of these animals to those of wild-type or heterozygous mutant mice. These experiments revealed that PAR bZip proteins control the expression of many enzymes and regulators involved in detoxification and drug metabolism, such as cytochrome P450 enzymes, carboxylesterases, and constitutive androstane receptor (CAR). Indeed, PAR bZip triple knockout mice are hypersensitive to xenobiotic compounds, and the deficiency in detoxification may contribute to their early aging.

Amino Acid Sequence↗
PubMed2000

Forskolin induces circadian gene expression of rPer1, rPer2 and dbp in mammalian rat-1 fibroblasts.

Mammalian culture cells have the potential for periodicity, since high concentrations of serum can elicit the circadian expression of clock genes in rat-1 fibroblasts. However, the mechanism by which serum affects circadian gene expression remains unclear. In the present study, we incubated rat-1 cells with forskolin and successfully induced the rhythmic expression of Per1, Per2 and dbp. In the initial step of the circadian gene expression, a marked transient induction of Per1 was observed accompanied with CREB phosphorylation. Thus the present study strongly suggests that CREB activation through the cAMP/PKA pathway is involved in the generation of circadian rhythm in rat-1 cells

Activating Transcription Factor 2↗
PubMed1994

Retinoblastoma control element binding proteins are induced during in vivo terminal differentiation of the liver and bind to the DBP promoter.

Growth regulation of terminal differentiation was studied by analysis of the promoter of the transcription factor D-site binding protein (DBP) using nuclear extracts from rat liver undergoing regeneration or from normal liver early in development. Four proximal binding sites for nuclear proteins were identified, three of which showed significant quantitative or qualitative changes in associated factors upon growth induction. Two of these sites bound factors common to the retinoblastoma control element and these proteins were induced upon terminal differentiation of the liver. These factors were also rapidly down-regulated upon induction of regenerative growth and consequent dedifferentiation. These results provide a link between the regulation of growth and differentiation in an in vivo model system.

Animals↗
PubMed2004

Rhythmic expression of DEC1 and DEC2 in peripheral tissues: DEC2 is a potent suppressor for hepatic cytochrome P450s opposing DBP.

The mammalian master molecular clock consisting of several clock gene products in the suprachiasmatic nucleus (SCN) drives circadian rhythms in behaviour and physiology. Molecular clocks consisting of the same components also exist in various peripheral organs. DEC1 and DEC2, basic helix-loop-helix transcription factors, were recently reported to be involved in the central clock in the SCN. We examined the expression profile of DEC1 and DEC2 in the periphery and their roles in the regulation of oscillating target genes in the liver. Levels of DEC1 and DEC2 mRNA exhibited a day-night variation in various peripheral tissues of rats. In the liver, their expression was high during the subjective night. Transfection assays showed that DEC2, but not DEC1, suppressed the transcription of the cholesterol 7alpha-hydroxylase gene (CYP7A), overwhelming the potent enhancement by D-site binding protein (DBP). Electrophoretic mobility shift assays indicated that DEC2 binds to the E-box (CACATG) at the -219/-214 region of CYP7A. The transcriptional activities of the other sterol metabolizing cytochrome P450s (Cyps), CYP8B and CYP51, were also suppressed by DEC2 but not DEC1. DEC2, but not DEC1, works as a direct output mediator that transmits the circadian signals to the hepatic functions, including the CYP7A, CYP8B, and CYP51 expression.

Animals↗
PubMed2006

Decreased serum free testosterone in workers exposed to high levels of di-n-butyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP): a cross-sectional study in China.

BACKGROUND: Observations of adverse developmental and reproductive effects in laboratory animals and wildlife have fueled increasing public concern regarding the potential for various chemicals to impair human fertility. OBJECTIVE: Our objective in this study was to assess the effect of occupational exposure to high levels of phthalate esters on the balance of gonadotropin and gonadal hormones including luteinizing hormone, follicle-stimulating hormone, free testosterone (fT), and estradiol. METHODS: We examined urine and blood samples of 74 male workers at a factory producing unfoamed polyvinyl chloride flooring exposed to di-n-butyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP) and compared them with samples from 63 male workers from a construction company, group matched for age and smoking status. RESULTS: Compared to the unexposed workers, the exposed workers had substantially and significantly elevated concentrations of mono-n-butyl phthalate (MBP; 644.3 vs. 129.6 microg/g creatinine, p < 0.001) and mono-2-ethylhexyl phthalate (MEHP; 565.7 vs. 5.7 microg/g creatinine, p < 0.001). fT was significantly lower (8.4 vs. 9.7 microg/g creatinine, p = 0.019) in exposed workers than in unexposed workers. fT was negatively correlated to MBP (r = -0.25, p = 0.03) and MEHP (r = -0.19, p = 0.095) in the exposed worker group. Regression analyses revealed that fT decreases significantly with increasing total phthalate ester score (the sum of quartiles of MBP and MEHP; r = -0.26, p = 0.002). CONCLUSION: We observed a modest and significant reduction of serum fT in workers with higher levels of urinary MBP and MEHP compared with unexposed workers.

Adult↗
PubMed1994

Developmental changes in the expression of the liver-enriched transcription factors LF-B1, C/EBP, DBP and LAP/LIP in relation to the expression of albumin, alpha-fetoprotein, carbamoylphosphate synthase and lactase mRNA.

Expression of alpha-fetoprotein, carbamoylphosphate synthase and albumin, that are generally accepted markers for the hepatic phenotype, require a distinct set of transcription factors. We investigated by in situ hybridization whether this set of transcription factors, LF-B1, C/EBP, DBP and LAP/LIP, is expressed coordinately in the liver during embryonic development and to what extent they are also expressed elsewhere. Our results demonstrate that mRNA levels of all transcription factors tested are significantly above background in the whole embryo and are either reduced or enhanced in expression during subsequent development. Interestingly, cardiac mesoderm, which induces prehepatic endoderm to liver formation, is temporarily permissive to its own signals, showing enhanced expression of these transcription factors and, as a result, the hepatocyte-specific genes alpha-fetoprotein and carbamoylphosphate synthase. In addition, these transcription factors and many liver-specific structural genes rise concomitantly in intestine and kidney just before birth, suggesting the expression of hepatogenic factors in these tissues as well. Despite the extrahepatic expression of these transcription factors, expression of albumin remains confined to the liver at all developmental stages.

Albumins↗
PubMed1993

Molecular evaluation of an Alu repeat including a polymorphic variable poly(dA) (AluVpA) in the vitamin D binding protein (DBP) gene.

We investigated an Alu element at the end of intron 8 of the human vitamin D-binding protein (hDBP, group-specific component, GC) gene that shows a polymorphic poly(A) tail due to a variable number of tandem repeats (AluVpA) forming the 3' end of this member of the most abundant class of short interspersed repeated DNA element (SINES). The Alu element sequence in intron 8 of the GC gene was identical in all three common GC alleles (GC*1F, GC*1S, and GC*2) and could be classified as an Alu-Sa or Alu class-II sequence. The polymerase chain reaction was used to amplify selectively a fragment of about 200 bp containing the identified (TAAA)n repeat from genomic DNA of 188 unrelated human subjects. The size of the amplified products was determined by polyacrylamide gel electrophoresis. Four alleles (named GC-18*6, GC-I8*8, GCI8*10, and GC-18*11) were found that differed in size by multiples of four nucleotides. The allele frequencies ranged from 0.0053 to 0.8511 and the observed heterozygosity was 26%. The stable inheritance of this polymorphic patterned poly(A) sequence was confirmed by a segregation study of a highly informative family with 19 members. Statistically significant linkage disequilibrium between the AluVpA and the GC iso-electric focusing (IEF) phenotypes was found in a sample of 188 unrelated individuals and delta values were calculated from the observed haplotype distribution.

Base Sequence↗
PubMed1985

Unusual sialilation of three different rare genetic variants of serum DBP: Gc1A17, Gc1A16, and Gc1A11.

The proteins of three anodal Gc1 variants, Gc1A16, 1A11, and 1A17, are characterized by the most acidic isoelectric points observed so far among the different Gc mutants. Stepwise removal of N-acetylneuraminic acid (NANA) by treatment with neuraminidase was performed to estimate the degree of sialilation of these Gc variants. The results indicate that both proteins, the anodal and the cathodal component of these Gc1 mutants, carry sialic acid residues. This observation is remarkable in so far as usually only the anodal component of the Gc1 protein contains NANA and only a single residue. From the experiments carried out it can be deduced that Gc1A16 has two NANA residues in the anodal and one NANA residue in the cathodal component. Gc1A16 was found in four members of three generations in a Danish family; the variant segregated as a Mendelian trait. More difficult to interpret are the results obtained with the variants Gc1A11 and Gc1A17. Gc1A11 probably has three NANA residues in the anodal and two NANA residues in the cathodal component. Gc1A11 has been observed in two mother-child pairs and is presumably also a simple genetic trait. Gc1A17 has also several NANA residues in both Gc proteins; it is suggested that the anodal component has either three or four NANA residues and the cathodal component either two or three NANA residues. Family information on this variant is not yet available.

Alleles↗