Molecular organization of the human Raf-1 promoter region

Three-dimensional culture regulates Raf-1 expression to modulate fibronectin matrix assembly

Oncogenic transformation has been associated with decreased fibronectin (FN) matrix assembly. For example, both the HT-1080 fibrosarcoma and MAT-LyLu cell lines fail to assemble a FN matrix when grown in monolayer culture (2-dimensional [2D] system). In this study, we show that these cells regain the ability to assemble a FN matrix when they are grown as aggregates (3-dimensional [3D] system). FN matrix assembly in 3D correlates with decreased Raf-1 protein expression compared with cells grown in monolayer culture. This effect is associated with reduced Raf-1 mRNA levels as determined by quantitative RT-PCR and not proteasome-mediated degradation of endogenous Raf-1. Interestingly, transient expression of a Raf-1 promoter-reporter construct demonstrates increased Raf-1 promoter activity in 3D, suggesting that the transition to 3D culture may modulate Raf-1 mRNA stability. Finally, to confirm that decreased Raf-1 expression results in increased FN matrix assembly, we used both pharmacological and small interfering RNA knockdown of Raf-1. This restored the ability of cells in 2D culture to assemble a FN matrix. Moreover, overexpression of Raf-1 prevented FN matrix assembly by cells cultured in 3D, resulting in decreased aggregate compaction. This work provides new insight into how the cell microenvironment may influence Raf-1 expression to modulate cell-FN interactions in 3D.

Independent control of cell survival by Raf-1 and Bcl-2 at the mitochondria

Bcl-2 family proteins play a critical role in the regulation of cell survival by controlling the activation of the cell death executing caspase machinery. Recent work demonstrated that they also provide a link between growth factor signaling and cell survival control. Raf-1 has been identified initially as an essential component of the mitogenic Ras-Raf-MEK-ERK cascade. However, expression of oncogenic Raf-1 also efficiently suppresses apoptotic cell death. This process requires mitochondrial translocation of Raf-1 which can be achieved either by co-expression of the anti-apoptotic protein Bcl-2 or by fusion with the transmembrane domain of the yeast outer mitochondrial membrane protein Mas 70p. It is currently unclear how mitochondrial Raf-1 prevents apoptosis. One possible mechanism involves the phosphorylation of the pro-apoptotic protein Bad resulting in the restoration of Bcl-2 function. Alternatively, the role of Bcl-2 could be limited to the mitochondrial translocation of Raf-1 and survival signaling by Raf-1 is Bcl-2 independent. To test for the mutual requirement of Raf-1 and Bcl-2 in apoptosis suppression the individual proteins were singly tested for survival activity in a genetic background which precludes the expression of the other. The results obtained in these studies demonstrate that ablation of Raf-1 or Bcl-2 expression in fibroblast cells significantly increases the sensitivity towards doxorubicin induced cell death. Reversion of the mutant phenotype could be achieved in either case by introducing a functional bcl-2 gene or a mitochondria targeted version of oncogenic Raf-1, demonstrating that each protein by itself is sufficient to confer protection. Our data thus suggest the existence of two separate pathways of survival signaling at the mitochondria controlled either by Bcl-2 or by Raf-1.

Comparative feline genomics: a BAC/PAC contig map of the major histocompatibility complex class II region

The genome organization of the human major histocompatibility complex (MHC) will be best understood in a comparative evolutionary context. We describe here the construction of a physical map for the feline MHC. A large-insert domestic cat genomic DNA library was developed using a P1 artificial chromosome (PAC) with a genomic representation of 2.5x and an average insert size of 80 kb. A sequence-ready 660-kb bacterial artificial chromosome/PAC contig map of the domestic cat MHC class II region was constructed with a gene order similar to, but distinct from, that of human and mice: DPB/DPA, Ring3, DMB, TAP1, DOB, DRB2, DRA3, DRB1, DRA2, and DRA1. Fluorescence in situ hybridization analyses of selected class II PAC clones confirmed that the class II region lies in the pericentromeric region of cat chromosome B2. However, apparently unlike the human and mouse MHCs, the domestic cat DRA and DRB genes have undergone multiple duplications and the DQ region has been deleted.

Two PDZ domain proteins encoded by the murine periaxin gene are the result of alternative intron retention and are differentially targeted in Schwann cells

Periaxin was first described as a 147-kDa protein that was suggested to have a potential role in the initiation of myelin deposition in peripheral nerves based upon its abundance, cell type specificity, pattern of developmental expression, and localization (Gillespie, C. S., Sherman, D. L., Blair, G. E., and Brophy. P. J. (1994) Neuron 12, 497-508). Here we show that the murine periaxin gene spans 20.6 kilobases and encodes two mRNAs of 4.6 and 5.2 kilobases that encode two periaxin isoforms, L-periaxin and S-periaxin of 147 and 16 kDa respectively. The larger mRNA is produced by a retained intron mechanism that introduces a stop codon and results in a truncated protein with an intron-encoded C terminus of 21 amino acids. Both proteins possess a PDZ domain at the N terminus; nevertheless, they are targeted differently in Schwann cells. Like other proteins that contain PDZ domains, L-periaxin is localized to the plasma membrane of myelinating Schwann cells: in contrast, S-periaxin is expressed diffusely in the cytoplasm. This suggests that proteins that contain this protein-binding module may also participate in protein-protein interactions at sites other than the cell cortex.

The interferon gamma (IFN-gamma) receptor: a paradigm for the multichain cytokine receptor

With the purification and cloning of the interferon gamma (IFN-gamma) receptor chains the mechanism of IFN-gamma action and the resultant signal transduction events were delineated in remarkable detail. The interferon gamma (IFN-gamma) receptor complex consists of two chains: IFN-gammaR1, the ligand-binding chain, and IFN-gammaR2, the accessory chain. Binding of IFN-gamma causes oligomerization of the two IFN-gamma receptor subunits, IFN-gammaR1 and IFN-gammaR2, which initiates the signal transduction events: activation of Jak1 and Jak2 receptor associated protein tyrosine kinases, phosphorylation of the IFN-gammaR1 intracellular domain on Tyr440 followed by phosphorylation and activation of Stat1alpha, the latent transcriptional factor. With all these steps established, the IFN-gamma receptor complex has provided the basic model for understanding the receptors for other members of the family of class II cytokine receptors.

The mouse extracellular signal-regulated kinase 2 gene. Gene structure and characterization of the promoter

ERK2 (extracellular-signal regulated kinase 2, also known as p42 mitogen-activated protein kinase) is an integral member of the mitogen-activated protein kinase cascade that is crucial for many cellular events such as proliferation and differentiation. Here, we determined the genomic organization of the Erk2 gene and characterized its promoter. The Erk2 gene spans over 60 kilobases, and the coding region is split into eight exons. In the coding region, exon-intron organization was exactly conserved between the two mouse genes for ERK2 and ERK1 except one junction shifted by one nucleotide. Primer extension and S1 nuclease analyses identified two major transcription start sites located at -219 and -223 relative to the translation start site. The 5'-flanking sequence lacked TATA box but contained a CCAAT box located approximately 60 base pairs upstream of transcription start sites. Sequencing of the 5'-flanking region also revealed potential cis-acting elements for multiple transcriptional regulatory factors including Sp1, zif268, Ets, CREB, and PuF sites. The promoter activity of the 5'-flanking region was examined using chloramphenicol acetyltransferase as a reporter gene. Transient transfection experiments using Chinese hamster ovary cells defined a maximal promoter activity in a 371-base pair region immediately upstream of the translation start site. Furthermore, we demonstrated, using mouse P19 embryonal carcinoma cells, that this 371-base pair sequence is likely to be sufficient to confer the transcriptional activation of the ERK2 promoter during the retinoic acid-induced differentiation of P19 cells.

The structure of the gene for murine CTP:phosphocholine cytidylyltransferase, Ctpct. Relationship of exon structure to functional domains and identification of transcriptional start sites and potential upstream regulatory elements

Phosphatidylcholine (PC) is the most abundant eukaryotic phospholipid and serves critical structural and cell-signaling functions. CTP:phosphocholine cytidylyltransferase (CT) is the rate-limiting enzyme in the CDP-choline pathway of PC biosynthesis, which is utilized by all tissues and is the sole or major PC biosynthetic pathway in all non-hepatic cells. Herein, we present the complete structure of the murine CT (Ctpct) gene. One P1 genomic clone and six subsequent plasmid subclones were isolated and analyzed for the exon-intron organization of the Ctpct gene. The gene spans approximately 26 kilobases and is composed of 9 exons and 8 introns. The exons match the distinct functional domains of the CT enzyme: exon 1 is untranslated; exon 2 codes for the nuclear localization signal domain; exons 4-7 encompass the catalytic domain; exon 8 codes for the alpha-helical membrane-binding domain; and exon 9 includes the C-terminal phosphorylation domain. Two transcriptional initiation sites, spaced 35 nucleotides apart, were identified using 5'-rapid amplification of cDNA ends polymerase chain reaction. The 5' natural flanking region was found to lack TATA or CAAT boxes and to contain GC-rich regions, which are features typical of promoters of housekeeping genes. Several sites that have the potential to interact with transcription regulatory factors, such as Sp1, AP1, AP2, AP3, Y1, and TFIIIA, were identified in the 5'-region of the gene and found to be distributed in two distinct clusters. These data will provide the basis for future studies on the cis- and trans-acting factors involved in Ctpct gene transcription and for the creation of induced mutant mouse models of altered CT activity.

The structure of the gene for the second chain of the human interferon-gamma receptor

The gene for the second chain of the human interferon-gamma receptor was analyzed from cosmid DNA clones. The gene spans over 33 kilobases of DNA and contains seven exons. The signal peptide is encoded by exons 1 and 2, the extracellular domain by exons 2, 3, 4, 5, and by part of 6. Exon 6 also encodes the whole transmembrane domain and part of the intracellular domain. Exon 7 encodes the remainder of the intracellular domain and contains the 3'-untranslated region. The sequences at the exon/intron boundaries are well conserved with respect to canonical acceptor/donor sites (AG/GT). The 5'-flanking region was sequenced and analyzed for transcription factor binding sites. No TATA or CAAT boxes in the promoter region were identified. Consistent with the lack of a TATA box, analysis of the mRNAs by primer extension showed multiple transcription start sites. Promoter activity of the 5'-flanking region was investigated with a luciferase reporter gene and the cytomegalovirus minimal promoter. Segments of the 5' region with promoter activity were identified.

Identification and analysis of the chicken c-mil promoter: possible involvement of Sp1- and Ets-related proteins

We have determined the exon organization in the 5' region of the chicken c-mil gene and identified its promoter. A 0.44-kb fragment containing the 5' terminus of the c-mil gene showed strong promoter activity when placed upstream of the bacterial chloramphenicol acetyltransferase gene and transfected into chicken embryo fibroblasts (CEF). By primer extension analysis, multiple transcriptional start sites were detected within the promoter region. Nucleotide sequence analysis revealed that the c-mil promoter had a high G + C content (71.8%) and contained multiple GC box-like sequences, but no TATA or CAAT boxes. Deletion analysis of 5' upstream sequences showed that the minimal region required for maximal promoter activity in CEF resides in the 99 bp located immediately upstream of the major initiation site. This region contains two putative Sp1 binding sites and one PU box/PEA3 motif, defined as a recognition element for members of the Ets gene family. These sequences bound proteins present in nuclear extracts of CEF as well as in vitro synthesized Ets-related proteins, suggesting that the binding of Sp1 or related proteins and of Ets-related proteins within the promoter is important for modulation of the mil gene.

Members of the raf gene family exhibit segment-specific patterns of expression in mouse epididymis

The proto-oncogene c-raf-1 and the related genes A-raf and B-raf encode serine/threonine protein kinases thought to be involved in regulating gene expression by acting as part of second-messenger signaling pathways within the cell. Among the tissues in which A-raf and c-raf-1 have been shown to be expressed was mouse epididymis. The present studies were undertaken to determine if the raf family genes exhibited specificity in their pattern of expression that might be indicative of specific function in the epididymis. Northern and in situ hybridization analyses demonstrated that c-raf-1 mRNA was expressed as a 3.1 kb transcript at uniform levels throughout the length of the epididymis in all types of epididymal epithelial cells. Neither the germ cell-specific testicular transcripts nor the somatic transcripts of B-raf were detected by either Northern or in situ hybridization analysis in any region of the epididymis. A-raf, expressed as two transcripts of 2.6 and 4.3 kb, was the only gene examined which exhibited a segment-specific pattern of expression, being highest in the principal epithelial cells of the proximal caput epididymis and decreasing progressively in more distal regions of the tubule. These studies indicate that each raf gene exhibits a characteristic pattern of expression in the epididymis; A-raf in particular may play a unique regulatory role in the regionalized functions of the epididymis.

Nucleotide sequence analysis of c-raf-1 cDNA and promoter from a radiation-resistant human squamous carcinoma cell line: deletion within exon 17

The c-raf-1 proto-oncogene is the cellular homologue of v-raf, the oncogene of the acutely transforming retrovirus 3611-MSV. The product of c-raf-1 (raf-1) is a 74-kDa cytoplasmic serine/threonine protein kinase. We previously reported that antisense human c-raf-1 cDNA transfection results in reduction of the endogenous c-raf-1 transcript, decreased tumor growth rate, and enhanced radiation sensitivity of SQ-20B tumor cells established from a radiation-resistant laryngeal squamous cell carcinoma. In the study reported here, we used cDNA-linked polymerase chain reaction amplification and nucleotide sequencing to examine the structure of the 3233-bp SQ-20B c-raf-1 cDNA. The 812-bp c-raf-1 promoter region was analyzed by genomic DNA amplification followed by cloning and sequencing. Sequence comparison with a previously published c-raf-1 sequence indicated no structural changes within the coding region of SQ-20B c-raf-1. However, a 4-bp deletion was observed in the 3' untranslated region within exon 17. This deletion was also present in a c-raf-1 cDNA clone isolated from a SQ-20B cDNA library. While the possibility of a 3' transcriptional control mechanism cannot be ruled out, it appears that the raf-1 protein kinase may regulate the development of radioresistant malignancies via interaction with other molecules in the damage and repair-related signal transduction pathways.

Expression of the Raf-1 protein in rat brain during development and its hormonal regulation in hypothalamus

To study mechanisms involved in the sexual differentiation of the rat brain, the expression of the protein product of the proto-oncogene c-raf-1 (Raf-1) was examined. Biochemical and immunocytochemical analyses localized Raf-1 in embryonic rat brain regions and demonstrated hormonally induced changes in Raf-1 expression. For this study an affinity-purified anti-peptide antiserum specific for Raf-1 (NH-44) was used. Western blots revealed an approximately 77 kD polypeptide isolated in the cytosol of developing rat brains. Raf-1 levels were highest in the embryonic (E) day 22 female hypothalamus (HYP), and approximately twofold higher than levels detected in male HYP at E22 as determined by quantitative protein dot blot and semiquantitative Western blot analyses. Raf-1 levels in HYP were greater than those in either brain stem (BS) or cortex. Immunocytochemical analysis revealed high levels of Raf-1 in selective brain regions (e.g., the ventromedial nucleus in the HYP, the mitral cell layers in the main and accessory olfactory bulbs (OB), and the locus coeruleus) at E22 and postnatal (P) day 1. Lower levels of immunoreactivity were observed in many areas of the perinatal neuraxis. To test hormonal regulation of Raf-1, testosterone propionate (TP) was administered to pregnant rats on E17; male and female fetuses were examined on E22. This treatment significantly decreased Raf-1 levels in female HYP, but not in male HYP, as determined by Western blot analysis. No significant sex difference or response to prenatal hormone treatments were observed in either brain stem or cortex. No significant sex difference was noted postnatally, and administration of TP 3 h after birth did not change Raf-1 levels examined 24 h later. In summary, Raf-1 was localized within selective regions of the rat brain, and its expression was altered by exogenous prenatal hormonal stimulation. One role for Raf-1 in signal transduction may be to delimit hormonal critical periods in sexual differentiation of the brain.

Molecular organization of the human cathepsin D gene

A 16-kb fragment of human DNA containing the cathepsin D (CATD) gene was isolated. Nucleotide sequencing, primer extension, protection from mung bean nuclease, and promoter activity assays were used to characterize the gene. The transcribed portion of the gene is about 11,000 bp and is organized into 9 exons analogous with the human pepsinogen A gene. Human pepsinogen A and CATD proteins have 42% sequence identity, while the two cDNAs are 55.7% identical. The positions of the splice junctions are fully conserved in these two genes. The noncoding sequences of the two genes are dissimilar. We report the nucleotide sequence of an Eco RI-Bam HI fragment that contains the transcription initiation site. The promoter region contains no TATA and CCAAT boxes, but five potential Sp1 binding sites (one of them in the first intron) and four AP-2 binding sites (two of them in the first intron). In COS-1 cells, the region containing the three proximal Sp1 sites possesses the bulk of the promoter activity of the 5'-flanking sequence. The transcription start site of the CATD gene is localized within a CpG cluster. In the interval -390 through +450, the content of CpG is 5.8 times above the average throughout the human genome.