Differential screening of murine ascites cDNA libraries by means of in vitro transcripts of cell-cycle-phase-specific cDNA and digital image processing

One single mRNA encodes the centrosomal protein CCD41 and the endothelial cell protein C receptor (EPCR)

The cDNA encoding the centrosomal protein CCD41 is identical with the cDNA for the endothelial cell protein C receptor. This finding is not due to an artefact, e.g. caused by selection of false positive clones. The segment of the CCD41 cDNA encoding the protein originally termed CCD41 and deletion mutants of it were fused with the nucleotide sequence encoding the enhanced green fluorescent protein (EGFP). Transfection and expression of the full length construct produces a fusion protein mainly located in cell membranes reflecting the receptor-type protein. Deletion mutants, e.g. those where the signal sequence is deleted, result in fusion proteins which are exclusively incorporated into a small perinuclear structure which is the site of the centrosome. This result suggests that post-translational modification, namely deletion of the signal sequence, is decisive for the centrosomal location of the resulting centrosomal protein while the unprocessed protein is incorporated into cell membranes.

Synergistic transcriptional activation of the mouse urokinase plasminogen activator (uPA) gene and of its enhancer activator protein 1 (AP1) site by cAMP and retinoic acid

We have investigated the mechanism whereby all-trans retinoic acid (tRA) potentiates the 8-bromo-cAMP (8-BrcAMP)-dependent transcription of the urokinase plasminogen activator (uPA) gene in SC115 mouse mammary carcinoma cells. Photoaffinity labelling experiments showed that tRA did not alter the cellular content of cAMP-dependent protein kinase regulatory subunits I and II. In agreement with this, nuclear run-on analysis in the presence of the translational inhibitor puromycin demonstrated that the effect of 8-BrcAMP and its potentiation by tRA were independent of protein synthesis. A transiently transfected 6.6 kb uPA 5'-flanking region-chloramphenicol acetyltransferase (CAT) fusion gene mimicked the response of the endogenous uPA gene. Thus 1 mM 8-BrcAMP induced a 100-200% increase in CAT content, 100 nM tRA had no effect and 100 nM tRA+1 mM 8-BrcAMP induced a 300-500% increase in cells co-transfected with tRA receptor and/or 9-cis-RA receptor. Analysis of 5'-deleted constructs showed that the tRA effect required at least two cis regions: -2657 to -2186, encompassing the 100 bp uPA enhancer, and -709 to -324, which exhibited silencing activity. Neither region contained a tRA-response element-like motif. Because tRA receptor and 9-cis-RA receptor interact with activator protein 1 (AP1), we tested whether tRA regulated the uPA enhancer AP1 site in the presence of 8-BrcAMP. We found that a dimer of this site fused to a minimal uPA-CAT fusion gene was responsive to 1 mM 8-BrcAMP (100% CAT increase), not responsive to 100 nM tRA, and synergistically responsive to 100 nM tRA+1 mM 8-BrcAMP (240% CAT increase) in cells co-transfected with Fos and Jun. Synergistic activation of the same construct and of the 6.6 kb uPA-CAT fusion gene was also obtained using tRA and 100 nM PMA. We conclude that multiple cis elements, probably including the uPA enhancer AP1 site, mediate the tRA potentiation of uPA transcription.

Protein analysis on a genomic scale

Methods for protein analysis, such as chromatography, electrophoresis, enzyme tests, receptor assays and immunological tests, have always been aimed in a classical reductionistic manner at investigating single proteins isolated from the complex protein composition of biological compartments. The complexity of the protein composition in biological systems was first visualized by two-dimensional electrophoresis (2-DE). Using 2-DE like a molecular microscope, protein variations between different biological situations may be detected by subtractive 2-DE analyses. Combining 2-DE with microsequencing, amino acid analysis and mass spectrometry protein spots on 2-DE gels may be identified. The sequence information can be used to find the gene. However, by 2-DE not only single protein changes can be detected and investigated on the gene level, but also complex changes of many proteins on a genomic scale.

Overexpression of the human NFM subunit in transgenic mice modifies the level of endogenous NFL and the phosphorylation state of NFH subunits

Neurofilaments (NFs), the major intermediate filaments of central nervous system (CNS) and peripheral nervous system (PNS) neurons, are heteropolymers formed from the high (NFH), middle (NFM), and low (NFL) molecular weight NF subunits. To gain insights into how the expression of NF subunit proteins is regulated in vivo, two transgenes harboring coding sequences for human NFM (hNFM) with or without the hNFM multiphosphorylation repeat domain were introduced into mice. Expression of both hNFM constructs was driven by the hNFM promoter and resulted in increased levels of hNFM subunits concomitant with an elevation in the levels of mouse NFL (mNFL) proteins in the CNS of both lines of transgenic mice. The increased levels of mNFL appear specific to NFM because previous studies of transgenic mice overexpressing either NFL or NFH did not result in increased expression of either of the other two NF subunits. Further, levels of the most heavily phosphorylated isoforms of mouse NFH (mNFH) were reduced in the brains of these transgenic mice, and electron microscopic studies showed a higher packing density of NFs in large-diameter CNS axons of transgenic versus wild-type mice. Thus, reduced phosphorylation of the mNFH carboxy terminal domain may be a compensatory response of CNS neurons to the increase in NFs, and reduced negative charges on mNFH sidearms may allow axons to accommodate more NFs by increasing their packing density. Taken together, these studies imply that NFM may play a dominant role in the in vivo regulation of the levels of NFL protein, the stoichiometry of NF subunits, and the phosphorylation state of NFH. NFM and NFH proteins may assume similar functions in regulation of NF packing density in vivo.

Expression of human cytokeratin 14 in normal, premalignant and malignant oral tissue following isolation by plaque differential hybridisation

Differences in gene transcription between RNA samples extracted from oral normal and squamous cell carcinoma (SCC) tissue were examined using the technique of cDNA library differential plaque screening. A differentially expressed transcript was selected on the basis of it being under-expressed in the cancer tissue and was identified, using DNA sequencing, as cytokeratin 14. The level of cytokeratin 14 transcription in RNA samples extracted from a range of oral SCC and normal tissue, as well as "white patch" lesions, was then investigated. Cytokeratin 14 appeared to be significantly under-expressed in oral cancer specimens studied compared to normal and white-patch tissue (P < 0.01). The trend for higher levels of cytokeratin 14 transcription in the dysplastic "white patch" samples compared to that observed for the malignant tissue (P < 0.05) suggests that the decrease in cytokeratin 14 transcription is a late event in the carcinogenic pathway.

Expression of mitochondrial genes and DNA-repair-related nuclear genes is altered in xeroderma pigmentosum fibroblasts

Differential hybridization was used to detect repair defects in xeroderma pigmentosum (XP) that are not amenable to current analyses. cDNA libraries were constructed from cytoplasmic RNA of normal and XP fibroblast strains (complementation groups A and D) and analyzed for differential gene expression. More than 40,000 lambda gt10 cDNA clones were differentially screened with in vitro transcripts made from cDNA in the pBluescript vector. Six differential clones were detected in the libraries of the XP group A and D strains which caused stronger or weaker signals when probed with transcripts from XP strains than with those from the normal strains. Two clones coded for mitochondrial genes: mitochondrial 16 S rRNA and ATPase 6L. Overexpression of mitochondrial genes in XP may indicate that functions of the ATP-generating system are impaired since such functions are intensified whenever they become insufficient, for example as a consequence of DNA damage. It is tempting to assume that abnormal mitochondria are one of the causes for the neurological malfunctions in XP. Furthermore, densitometric analysis of Northern blots revealed that mRNA of lactate dehydrogenase, chain M, was less abundant in four XP group A strains (extent of reduction: 70%) and in two XP group D strains (extent of reduction: 58%). Enzyme activity was also diminished. In addition, mRNA of the gene for glyceraldehyde-3-phosphate dehydrogenase was less expressed in the same XP group A and D fibroblast strains investigated (reduction in both complementation groups: 50%). Both glycolytic enzymes have nuclear functions apart from their role in sugar metabolism. Lactate dehydrogenase, chain M, is identical to a helix-destabilizing protein; it is closely associated with chromatin and unfolded DNA, suggesting a role in DNA synthesis and transcription. The 37-kDa subunit of glyceraldehyde-3-phosphate dehydrogenase is involved in transcription and was shown to be identical to uracil-DNA glycosylase, a base-excision repair enzyme. We presume that the nuclear functions of these glycolytic enzymes may be thwarted in the XP strains investigated and may account for malfunctions in XP, particularly for neurological disturbances.

Sequence of a complete murine cDNA reflecting an S phase-prevalent transcript encoding a protein with two types of nucleic acid binding motifs

Differential screening of a murine RNA-based lambda gt10 cDNA library with cell cycle phase-specific probes released a cDNA clone (lambda GS1) to a mRNA (1.8 kb) which is prevalent in the S phase of the cell cycle. The nucleotide sequence of the cDNA predicts a protein (RNPS1, 41 x 10(3) M(r) with two nucleic acid-binding domains separated by a proline-rich spacer. The N-terminal nucleic acid binding domain, about 80 amino acid residues in length, meets the requirements of an RNA recognition motif (RRM) including a perfect 'RNP-1 octamer'. The C-terminal nucleic acid binding domain spanning over 26 amino acid residues is prominent because it comprises three copies of the RRRS peptide. Domains of the latter type are considered to be involved in RNA and DNA-binding because comprised in many RNA and DNA-binding proteins.

Enhanced expression of mitochondrial genes in xeroderma pigmentosum fibroblast strains from various complementation groups

cDNA libraries constructed from cytoplasmic RNA of normal and xeroderma pigmentosum (XP) fibroblast strains were screened for differential gene expression. XP fibroblast strains included one representative of the complementation groups A, C, D, and one XP variant strain. The XP lambda gt10 cDNA libraries were differentially screened with in vitro transcripts made from cDNA in the pBluescript vector using both the same XP strain and the normal fibroblast strain. Eight differential clones were detected in the libraries of the XP group A, D, and C strains, which caused stronger signals when probed with transcripts from XP strains than with those from the normal strain. The cDNA clones were sequenced. Seven of the eight clones detected coded for three mitochondrial genes: subunit I of cytochrome c oxidase (complex IV of the respiratory chain), apocytochrome b (subunit of complex III), and 16-S rRNA. Two clones representing essentially (a) subunit I of cytochrome c oxidase and (b) 16-S rRNA diverged from the sequence of the human mitochondrial genome present in the data-base libraries. Clone a exhibited a transition mutation, clone b reflected a transcript of a mitochondrial genome rearranged in the 16-S rRNA gene, including four nucleotides of the adjacent tRNA(Leu) gene. The apparently enhanced expression of mitochondrial genes in XP cells, together with the changes in DNA sequence, seem to indicate that functions of the ATP-generating system were impaired. This defect may have originated from mutations due to lack of DNA repair. The data can be interpreted in the light of mitochondrial changes that cause human neuromyopathies to occur. In analogy to these diseases the neurological symptoms in XP might be explained by abnormal mitochondria.

cDNA-derived molecular characteristics and antibodies to a new centrosome-associated and G2/M phase-prevalent protein

Differential screening of a murine RNA-based cDNA library with cell cycle phase-specific transcripts released a cDNA clone (lambda CCD41) to a mRNA (1.349 kb) which, according to the mode of its detection, increases as expected during the cell cycle. The molecular characteristics of the protein (27 × 10(3) M(r)) encoded by this mRNA were deduced from the cDNA sequence and antibodies were prepared against the recombinant protein. Immunofluorescence studies performed with PtK2 cells revealed that the amount of the antigen specified by the CCD41 sequence increases during the cell cycle out of proportion with the DNA content. In G1 phase cells, the antigen is exclusively located at the site of the centrosome. During cell cycle progression the antigen becomes also detectable in perinuclear vesicles that increase in number and size, reaching a maximum in G2 phase cells. The centrosomal location of the CCD41 antigen was investigated in relation to another centrosomal antigen, centrosomin A. Since the latter antigen is detected by a monoclonal antibody reacting specifically and permanently with the centrosomes in PtK2 cells throughout the cell cycle it was possible to investigate the relative positions of the two proteins at the site of the centrosome and to add new information about the general architecture of the organelle and its changes during the cell cycle. While the centrosomin A antibody detects the pronounced cell cycle stage-dependent shape changes of the centrosome, the CCD41-encoded protein appears to be localized as a compact structure inside the centrosome. Its epitopes are exposed throughout the cell cycle except during a brief period immediately after the formation of the daughter centrosome.

Nucleotide sequence of the murine prothymosin alpha cDNA and its deduced primary and secondary protein structure

Searching for proliferation-related and cell cycle phase-specific genes we detected a full-length cDNA for the murine prothymosin alpha mRNA which was sequenced on the DNA level. The amino acid sequence deduced from the nucleotide sequence shows a high degree of positional identities with prothymosin alpha from man and rat. However, the minor differences in the primary structures largely influence predictions for the secondary structures of prothymosin alpha from different species. These differences in the secondary structure could explain the differences of activity of prothymosin alpha from different origin in immuno-protection assays.