Primary structure and assignment to chromosome 6 of three related rat genes encoding liver serine protease inhibitors

Recent segmental duplications in the working draft assembly of the brown Norway rat

We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1%-1.2%) but significantly less than that of human ( approximately 5%). Duplications were nonuniformly distributed, occurring predominantly as tandem and tightly clustered intrachromosomal duplications. Regions containing extensive interchromosomal duplications were observed, particularly within subtelomeric and pericentromeric regions. We identified 41 discrete genomic regions greater than 1 Mb in size, termed "duplication blocks." These appear to have been the target of extensive duplication over millions of years of evolution. Gene content within duplicated regions ( approximately 1%) was lower than expected based on the genome representation. Interestingly, sequence contigs lacking chromosome assignment ("the unplaced chromosome") showed a marked enrichment for segmental duplication (45% of 75.2 Mb), indicating that segmental duplications have been problematic for sequence and assembly of the rat genome. Further targeted efforts are required to resolve the organization and complexity of these regions.

Inflammation induces serine protease inhibitor 3 expression in the rat pineal gland

In the rat pineal gland, prominent expression of serine protease inhibitor 3 (SPI-3) mRNA is seen after systemic injection of lipopolysaccharide. The up-regulation of SPI-3 mRNA expression is also confirmed by northern blotting. Most SPI-3 mRNA-positive cells simultaneously express synaptophysin, a marker for pinealocytes, but not glial fibrillary acidic protein, a marker for astrocytes. This indicates that SPI-3 mRNA-positive cells are pinealocytes. Almost all SPI-3 mRNA-positive cells also showed translocation of the signal transducers and activators of transcription 3 (STAT3) into nuclei after lipopolysaccharide injection. These data support previous in vitro results that SPI-3 expression is induced in a STAT3-mediated manner. In addition, the expression of ciliary neurotrophic factor receptor (CNTFR) and leukemia inhibitory factor receptor (LIFR) mRNAs, but not of interleukin 6 receptor mRNA, was up-regulated after systemic lipopolysaccharide treatment. Because these receptors are upstream of STAT3, the present results suggest that cytokines such as LIF and/or CNTF induce SPI-3 expression via STAT3 in the pineal gland in response to inflammatory stimulus. We conclude that although the functional consequences of SPI-3 in the pineal gland during systemic inflammation are unknown, SPI-3 may have a crucial role in preventing some degenerative proteolysis induced by inflammatory stimuli.

Transcription of the rat serine protease inhibitor 2.1 gene in vivo: correlation with GAGA box promoter occupancy and mechanism of cytokine-mediated down-regulation

Two GH-response elements (GHREs) and a single glucocorticoid (GC)-response element were found to regulate activity of the rat serine protease inhibitor 2.1 gene (spi 2.1) promoter in vitro. To assess the physiological relevance of these observations, we have investigated the relationship existing between the level of spi 2.1 gene transcription, structural modifications of the chromatin, and in vivo nuclear protein-promoter interactions monitored by genomic footprinting, in control, hypophysectomized, and inflamed rats. We also addressed the mechanism of inflammation-mediated gene down-regulation. We found that a high level of spi 2.1 gene transcription correlates with hypersensitivity of the promoter to deoxyribonuclease I (DNase I) and maximal occupancy of the GAGA box (GHRE-I). The failure of GAGA-box binding proteins (GAGA-BPs) to interact with the GAGA box appears to result from an impairment in GH action due to its absence (i.e. hypophysectomized animals) or to the appearance of a cytokine-mediated GH-resistant state (i.e. inflamed rats) in liver. Unlike the GAGA box, signal transducer and activator of transcription (STAT) factor-binding sites included in the GHRE-II were never found to be protected against DNase I attack but displayed a differential DNase I reactivity depending on the level of gene transcription. Alterations in DNase I reactivity of the GC-response element region suggest that GC receptor-GC complexes may associate, in a transient manner, with the promoter in the actively transcribing control state. Taken together, our studies suggest a mechanism of spi 2.1 gene activation in vivo whereby the GH-dependent chromatin remodeling caused by or concomitant to the recruitment of GAGA-box binding proteins is the first compulsory and presumably predominant step.

Molecular cloning and expression of rat kallistatin gene

We have previously purified and cloned human kallistatin and rat kallikrein-binding protein (RKBP), which are tissue kallikrein inhibitors belonging to the serine proteinase inhibitor superfamily. In this study, we have cloned and sequenced the gene encoding rat kallistatin with Phe-Phe-Ser-Ala-Gln at positions P2-P3', which is identical to the reactive center of human kallistatin. Rat kallistatin is highly similar to human kallistatin, sharing 68% and 57% sequence identity at the cDNA and the amino acid levels. The rat kallistatin gene exists in a single copy and is located on chromosome 6. An SphI RFLP is found between SHR and WKY rats at or near the rat kallistatin gene locus. Two amino acid polymorphisms of the rat kallistatin gene between these two strains were found by sequence analysis. A candidate promoter in the 5'-flanking region (109 bp) of the rat kallistatin gene has been identified by reporter assays. The expression of rat kallistatin in the liver is growth-dependent and down-regulated during acute phase inflammation. Recombinant rat kallistatin produced in E. coli is able to bind to tissue kallikrein, and the interaction is inhibited by heparin. These characteristics define rat kallistatin as the counterpart of human kallistatin.

Tissue kallikrein inhibitors in mammals

We have discovered, purified and cloned a new kallikrein-binding protein (KBP or kallistatin) from humans and rodents. Kallistatins are members of the serine proteinase inhibitor (serpin) superfamily. They are acidic glycoproteins with molecular masses of 58-62 kDa and pI values of 4.6-5.2. Kallistatin forms a SDS-stable complex with tissue kallikrein and inhibits kallikrein's activities. Human kallistatin has a unique cleavage site with Phe-Phe-Ser at the P2-P1-P1' positions. The protein sequence of mature human kallistatin shares 44-46% identity with other serpins such as human alpha 1-antitrypsin, protein C inhibitor and rat kallikrein-binding protein. The kallistatin genes display the typical five exon-four intron serpin gene structure. The human kallistatin gene is localized on chromosome 14q31-32.1 and the RKBP gene is on chromosome 6. Kallistatin is evolutionarily diverse but functionally conserved in mammalian species. This overview summarizes the biochemistry, molecular biology and potential physiology and/or pathophysiology of this new tissue kallikrein inhibitor.

Two separate signal transducer and activator of transcription proteins regulate transcription of the serine proteinase inhibitor-3 gene in hepatic cells

The serine proteinase inhibitor (SPI-3) gene expression is transcriptionally regulated by interleukin (IL)-6 and glucocorticoids in hepatic cells. To identify the transcription factors involved in regulation of the SPI-3 promoter-chloramphenicol acetyltransferase constructs we overexpressed Signal Transducer and Activator of Transcription (STAT) proteins (STAT1, STAT3, STAT5B, and STAT6) and CAAT enhancer-binding protein beta. Specific signaling pathways were activated by cointroduced receptors for growth hormone, IL-3, IL-4, or chimeric receptors containing the cytoplasmic domain of gp130. STAT3 and STAT5B induced transcription via the SPI-3 promoter. The STAT5B response was substantially enhanced by truncation of the 5'-flanking region from -1021 to -148. The responsiveness to STAT3 and STAT5B required the STAT binding element at -132 to -124. This element was sufficient to confer regulation onto a heterologous promoter gene construct. In contrast, overexpression of CAAT enhancer-binding protein beta reduced the transcriptional activity of the SPI-3 promoter, presumably by interfering with STAT protein binding to the promoter element. The SPI-3 gene is the first example of an acute phase gene that is responsive to both STAT3 and STAT5B.

Regulation of expression of the rat serine protease inhibitor 2.3 gene by glucocorticoids and interleukin-6. A complex and unusual interplay between positive and negative cis-acting elements

The rat serine protease inhibitor 2.3 gene (spi 2.3) is almost completely silent in normal animals and is transiently expressed during acute inflammation. It encodes a potential anti-elastase which is likely to play a major physiological role for the host defense. Two well-known inflammatory mediators, glucocorticoids and interleukin-6 (IL-6) activate the spi 2.3 promoter and increase steady-state levels of mRNA in cultured hepatocytes. GC activation is mediated by a single glucocorticoid-response element which seems to act autonomously. A unique array of four functional IL-6-response sites was identified in the spi 2.3 promoter. Three of them (C-II--IV) bear structural identity to the CCAAT/enhancer-binding-protein-binding site consensus sequence, whereas the fourth closely resembles the consensus kappa B nuclear factor recognition motif. The C-IV element, which is the most active, contains the motif 5'-CTGGGA and binds the IL-6-inducible acute-phase response factor present in liver nuclear extracts from inflamed rats. Both basal and IL-6-dependent activities of each individual cytokine-response element tested separately are strongly down regulated by a recently identified regulatory sequence, located in the 3' untranslated region of the spi 2.3 gene. However, this repressor element does not significantly affect overall IL-6-dependent spi 2.3 promoter activity. This suggests that, in the context of the active gene in vivo, all four IL-6-response sites, which are largely redundant, cooperate to overcome the strong repressive effect of the 3' untranslated region silencer and are needed to bring about a maximal IL-6 response. These data reveal a novel type of regulation of an acute-phase gene involving different classes of IL-6-response elements controlled by a repressor and acting in conjunction with a glucocorticoid-response element.

The role of Stat and C/EBP transcription factors in the synergistic activation of rat serine protease inhibitor-3 gene by interleukin-6 and dexamethasone

The rat serine proteinase inhibitor 3 gene is activated by interleukin 6 (IL-6) and glucocorticoids in hepatic cells. We report here that a 147 bp promoter is sufficient for both IL-6 stimulation and glucocorticoid enhancement of IL-6 induced transcription. Within this region we identified two functional elements binding transcription factors from the C/EBP (CCAAT/enhancer binding proteins) and Stat (signal transducers and activators of transcription) families. Mutations introduced into the Stat binding site resulted in a loss of responsiveness, showing that this element is indispensable for activation. In contrast, the promoter containing the mutated C/EBP binding site was still responsive to IL-6 and glucocorticoids; however, the magnitude of the induction was decreased by 50%. The Stat binding element is an enhancer capable of conferring both responsiveness to IL-6 and partial enhancement of glucocorticoids on to a heterologous promoter. In response to IL-6 this element rapidly binds acute-phase response factor (APRF/Stat3) and, later, the protein(s) that require ongoing protein synthesis and is recognized by anti-Stat3 antibodies. In addition, long-term treatment with IL-6 results in sustained phosphorylation of APRF /Stat3.

Messages from an isolate: lessons from the Finnish gene pool

Genetic isolates are the result of some type of bottleneck in the history of a population, revealing the consequences of the founder effect and genetic drift on the population's gene pool. In human populations, isolation is suspected based on an exceptional geographic location or cultural history or on the prevalence of relatively rare genetic diseases. The concept of 'Finnish disease heritage' is well established in the literature, but solid data have only recently emerged regarding the uniformity of disease mutations at the molecular level in this population: for many Finnish diseases for which the molecular defect has been uncovered, over 90% of disease alleles carry the same causative mutation. This suggests dramatic isolation, especially in some subregions of the sparsely populated country. In Finland, this molecular information can be combined with the exceptional genealogical data offered by a well established church record system which dates back to 1640, containing detailed information on births, deaths, marriages and movements of the majority of the population. This provides excellent opportunities for special study designs for the identification not only of rare disease genes but also of major loci which contribute to complex diseases. The utilization of linkage disequilibrium and the search for shared haplotypes can be justified in subpopulations and patient materials from this genetic isolate. This review summarizes the current molecular evidence for genetic isolation as well as the utilization of some special strategies in the disease gene hunt in the Finnish population.

Growth hormone induction of hepatic serine protease inhibitor 2.1 transcription is mediated by a Stat5-related factor binding synergistically to two gamma-activated sites

A growth hormone (GH)-inducible nuclear factor (GHINF) from rat liver has been purified to near homogeneity. On SDS-polyacrylamide gel electrophoresis and UV-cross-linking, a major band of mass approximately 93 kDa and a minor band of approximately 70 kDa are detected in the purified fraction. DNase I footprinting using purified GHINF yields a protected region of -149/-115 on the rat serine protease inhibitor 2.1 (Spi 2.1) promoter encompassed within the growth hormone response element (GHRE). Mutational analysis demonstrated that GHINF binds synergistically to two gamma-interferon-activated sites (GAS) within the GHRE, with the 3' element being the pivotal binding domain. Functional assays show that both GAS elements are necessary for full GH response. GHINF has no immunoreactivity with either a C-terminal Stat1 antibody or an N-terminal Stat3 antibody, while cross-reacting with a C-terminal Stat5 monoclonal antibody. GHINF will bind to two GAS elements from the Stat5 binding region of the beta-casein gene. These studies indicate that GHINF is a Stat5-related factor binding synergistically to two GAS elements to activate Spi 2.1 transcription.

Activation of the rat serine proteinase inhibitor 3 gene by interferon gamma via the interleukin 6-responsive element

Transcription of rat serine proteinase inhibitor 3 (SPI-3) gene is rapidly induced in the liver in response to inflammation. Treatment of rat hepatoma H-35 cells with interferon gamma (INF gamma) results in the immediate induction of this gene, with its 147 bp-long promoter being sufficient for activation. Within this promoter we have identified an IFN gamma-responsive element which maps to the signal transducer and activator of transcription (Stat)3-binding site. Mutation of this element causes a loss of responsiveness to IFN gamma, whereas fusion to a heterologous promoter confers a positive response on IFN gamma. The latter apparently induces the binding of a protein, identified as Stat1, to the described element, which gradually decreases within 24 h. Thus the induction of the SPI-3 gene by IFN gamma correlates with the binding of Stat1 to a specific element which, in turn, binds Stat3 in response to interleukin 6.

Spi-1: an hepatic serine protease inhibitor regulated by GH and other hormones

A sensitive RNAse protection method was used to show that serine protease inhibitor-1 (Spi-1) is expressed in rat liver and heart, but not in kidney or brain. Bovine somatotropin (bGH) and placental lactogen (bPL) induced rat hepatocyte cultures to express both Spi-1 and IGF-1 mRNA, with bPL approximately 100-fold more potent than bGH. Bovine prolactin (bPrL) did not induce hepatocyte Spi-1 mRNA, demonstrating lack of involvement of lactogenic receptors. Albumin mRNA levels were stable during hepatocyte culturing and were unaffected by growth hormone (GH) treatment, showing that neither culture conditions nor GH treatment affected cellular differentiation. Eliminating serum-free medium hormone supplements one at a time, estradiol, testosterone and T3 were shown to be unnecessary for GH induction of Spi-1, while dexamethasone removal decreased Spi-1 mRNA levels to 10% of GH-stimulated controls. bGH induction of Spi-1 mRNA in the presence of only dexamethasone and glucagon was 75% higher (p < 0.01) than levels seen with insulin also present.

Regulation of two rat serine-protease inhibitor gene promoters by somatotropin and glucocorticoids. Study with intact hepatocytes and cell-free systems

Only two out of the three serine-protease inhibitor genes (SPI 2.1, 2.2 and 2.3) expressed in rat liver are tightly controlled by somatotropin acting mainly at the transcriptional level, thus making this gene system particularly suitable to study its molecular mechanism of action. In these studies, we analyzed SPI promoter activities in cultured hepatocytes transfected by electroporation or in cell-free extracts. The proximal SPI 2.1 promoter region contains two somatotropin-responsive sites which are functional in intact cells. The more distal element that maps at positions -175 to -114, and is analogous to the one originally described by Yoon et al. (1990) [Yoon, J. B., Berry, S. A., Seelig, S. & Towle, H. C. (1990) J. Biol. Chem. 265, 19947-19954], behaves as a weak enhancer whose activity is strongly potentiated by proximal 5' downstream sequences that contains potential CCAAT-enhancer binding protein (C/EBP) sites. An additional proximal hormone-sensitive site is located in the close vicinity of the transcription-start site between positions -41 and +8, and also requires the first C/EBP-binding element to be active. The distal element appears to contribute more importantly (60%) than the proximal one (40%) to the overall somatotropin stimulation of chimeric gene expression. Nonetheless, both displayed similar dose-dependence, with half-maximal and maximal effects occurring at 0.5-1 nM and 5-10 nM, respectively. The somatotropin refractoriness of the SPI 2.3 gene appears to be due to the presence of distal (-2300 to -200) inhibitory element(s) in the promoter. Glucocorticoids exert both positive and negative effects on SPI promoter activity. Their stimulatory action appears to involve sequences located between positions -114 and -82, together with a more distal half glucocorticoid-responsive element, whereas their inhibitory effect is more likely mediated by sequences located between positions -41 and +8. In vitro transcription assays, performed with promoter-deletion mutants and competitor oligonucleotides, revealed the presence of a major functional C/EBP site located immediately upstream from the transcription-start point. Unfortunately, the regulatory features of SPI gene expression observed in intact cells were completely obliterated by breaking down the cell structure, and could not therefore be studied using cell-free systems.

Electroporation-mediated gene transfer into hepatocytes: preservation of a growth hormone response

An electroporation procedure is described which allows the introduction of foreign genes into freshly isolated rat hepatocytes while preserving their growth hormone responsiveness. A single-pulse procedure performed at low voltage (150-200 V) but with high capacitance (960 microF), conditions which caused minimal cell damage and increased hepatocyte survival in culture (greater than 80%), was found to be optimal for both the basal and the hormone-stimulated expression of transfected genes. Transfection of the cells suspended in a phosphate buffer at high concentrations (20-25 x 10(6)/ml) with large amounts of plasmid (30 micrograms/assay) gave the best results. Raising the temperature up to 25 or 37 degrees C (instead of 4 degrees C) decreased about twofold basal CAT expression but appeared to increase the magnitude (i.e., fold induction) of hormonal effects. Expression of the reporter gene driven by either a viral or a liver gene promoter reached a maximum after 24 h, a situation especially favorable when studying liver-specific gene expression known to decay rapidly in cultured hepatocytes. This procedure was successfully applied to the study of a growth hormone-dependent serine protease inhibitor gene promoter.

Analysis of proteins binding to the proximal promoter region of two rat serine protease inhibitor genes

The three serine protease inhibitor (SPI) rat genes expressed preferentially in liver share considerable structural features and, nonetheless, are transcriptionally regulated in completely different manners, more particularly after hypophysectomy or upon acute inflammation. DNase I footprinting and gel mobility shift analyses of the SPI 2.1 and 2.3 proximal promoter regions reveal the presence of three common protein binding sites (1 to 3, 3' to 5') located immediately upstream from the transcription start site. C/EBP, the liver-enriched factor, specifically interacts with site 1 whereas its related proteins (e.g.; DBP, LAP/NFIL6) most likely recognize sites 2 and 3. Another ubiquitous unidentified factor also binds to site 2. A liver-specific protein dependent on growth hormone, whose binding is competed out by an oligonucleotide reproducing an HNF3 motif, interacts exclusively with site 3. The 42 bp sequence which is found only within the SPI 2.3 promoter interacts with two ubiquitous factors, one of which is related to NF kappa B. Acute inflammation does not significantly affect the protein binding patterns observed with the SPI 2.1 or 2.3 proximal promoter sequences. Our results show an apparent discrepancy between the large magnitude of in vivo changes in SPI gene transcription mediated by hormones and the small alterations detected in vitro, in the DNA-protein interactions on the promoters.

Developmental regulation of the hepatic acute phase response

For evaluation of the ontogenetic regulation of the acute phase response, inflammation was induced in Fischer rat litters at different postnatal ages. Four homologous rat hepatic serine protease inhibitor (Spi 2.1, Spi 2.2, Spi 2.3, and alpha 1-antitrypsin) mRNAs were measured in livers 24 h after injection. Animals mounted both positive and negative acute phase responses at all ages, but responses were blunted in young animals, reaching adult levels by days 7-19. alpha 1-Antitrypsin mRNA had no response, and Spi 2.2 mRNA had 50% the rise seen in adults on days 3 and 7. Spi 2.1 and 2.3 mRNAs, negative acute phase reactants, showed attenuation of adult response to inflammation in infant animals of 33% (Spi 2.1) and 40% (Spi 2.3). In hypophysectomized animals, the responses of Spi 2.2, 2.3, and alpha 1-antitrypsin mRNAs after turpentine stimulation were similar to that of normal animals, whereas Spi 2.1 mRNA did not change. In conclusion, infant animals mount a blunted response to tissue injury; multiple factors may be involved in the development of the full adult response. Immaturity of the pituitary may play a role in the suppression of Spi 2.1 mRNA's response during inflammation in infant animals. These highly evolutionary related genes will be helpful in identifying specific factors regulating gene expression in inflammation and development.

The gene map of the Norway rat (Rattus norvegicus) and comparative mapping with mouse and man

The current status of the rat gene map is presented. Mapping information is now available for a total of 214 loci and the number of mapped genes is increasing steadily. The corresponding number of loci quoted at HGM10 was 128. Genes have been assigned to 20 of the 22 chromosomes in the rat. Some aspects of comparative mapping with mouse and man are also discussed. It was found that there is a good correlation between the morphological homologies detectable in rat and mouse chromosomes, on the one hand, and homology at the gene level on the other. For 10 rat synteny groups all the genes so far mapped are syntenic also in the mouse. For the remaining rat synteny groups it appears that the majority of the genes will be syntenic on specific (homologous) mouse chromosomes, with only a few genes dispersed to other members of the mouse karyotype. Furthermore, the data indicate that mouse chromosome 1 genetically corresponds to two rat chromosomes, viz., 9 and 13, equalizing the difference in chromosome number between the two species. Further mappings will show whether the genetic homology will prove to be as extensive as these preliminary results indicate. As might be expected from evolutionary considerations, rat synteny groups are much more dispersed in the human genome. It is clear, however, that many groups of genes have remained syntenic during the period since man and rat shared a common ancestor. One further point was noted. In two cases groups of genes were syntenic in the mouse but dispersed to two chromosomes in rat and man, whereas in a third case a group of genes was syntenic in the rat but dispersed to two chromosomes in mouse and man. This finding argues in favor of the notion that the original gene groups were on separate ancestral chromosomes, which have fused in one rodent species but remained separate in the other and in man.