Functional analysis of adenovirus protein IX identifies domains involved in capsid stability, transcriptional activity, and nuclear reorganization.

The product of adenovirus (Ad) type 5 gene IX (pIX) is known to actively participate in the stability of the viral icosahedron, acting as a capsid cement. We have previously demonstrated that pIX is also a transcriptional activator of several viral and cellular TATA-containing promoters, likely contributing to the transactivation of the Ad expression program. By extensive mutagenesis, we have now delineated the functional domains involved in each of the pIX properties: residues 22 to 26 of the highly conserved N-terminal domain are crucial for incorporation of the protein into the virion; specific residues of the C-terminal leucine repeat are responsible for pIX interactions with itself and possibly other proteins, a property that is critical for pIX transcriptional activity. We also show that pIX takes part in the virus-induced nuclear reorganization of late infected cells: the protein induces, most likely through self-assembly, the formation of specific nuclear structures which appear as dispersed nuclear globules by immunofluorescence staining and as clear amorphous spherical inclusions by electron microscopy. The integrity of the leucine repeat appears to be essential for the formation and nuclear retention of these inclusions. Together, our results demonstrate the multifunctional nature of pIX and provide new insights into Ad biology.

Genomic structure and chromosomal mapping of the gene coding for ICBP90, a protein involved in the regulation of the topoisomerase IIalpha gene expression.

We have recently identified a novel CCAAT box binding protein (ICBP90) involved in the regulation of topoisomerase IIalpha gene expression. We have observed that it is expressed in non-tumoral proliferating human lung fibroblast cells whereas in HeLa cells, a tumoral cell line, ICBP90 was still present even when cells were at confluence. In the present study, we have determined the ICBP90 gene structure by screening of a human placenta genomic library and PCR analysis. We report that the ICBP90 gene spans about 35.8 kb and contains six coding exons named A to F. In the 5' upstream sequence of the region containing the coding exons, two additional exons (I and II) were found. Additionally, an internal splicing site was found in exon A. A promoter region, including three putative Sp1 binding sites between exons I and A, was identified by transient transfection. Northern blot analysis of several cancer cell lines revealed the existence of two ICBP90 mRNA species of 5.1 and 4.3 kb that are transcribed from the gene. The relative amounts of these mRNAs depended on the cell type. In MOLT-4 cells and Burkitt's lymphoma Raji cells, the 4.3 kb or the 5.1 kb transcripts were mainly observed, respectively. In other cell lines, such as HL-60 cells, chronic myelogenous leukaemia K-562, lung carcinoma A549, HeLa or colorectal SW480, both 4.3 and 5.1 kb forms of ICBP90 mRNA could be detected. Interestingly, western blot analysis showed several ICBP90 protein bands in HeLa but only a single band in MOLT-4 cell extracts. Taken together our results are consistent with the ICBP90 gene exhibiting alternative splicing and promoter usage in a cell-specific manner.

Cell cycle regulation of the endogenous wild type Bloom's syndrome DNA helicase.

Bloom's syndrome (BS) is a rare human autosomal recessive disorder characterized by an increased risk to develop cancer of all types. BS cells are characterized by a generalized genetic instability including a high level of sister chromatid exchanges. BS arises through mutations in both alleles of the BLM gene which encodes a 3' - 5' DNA helicase identified as a member of the RecQ family. We developed polyclonal antibodies specific for the NH2- and COOH-terminal region of BLM. Using these antibodies, we analysed BLM expression during the cell cycle and showed that the BLM protein accumulates to high levels in S phase, persists in G2/M and sharply declines in G1, strongly suggestive of degradation during mitosis. The BLM protein is subject to post-translational modifications in mitosis, as revealed by slow migrating forms of BLM found in both demecolcine-treated cells and in mitotic cells isolated from non-treated asynchronous populations. Phosphatase treatment indicated that phosphorylation events were solely responsible for the appearance of the retarded moieties, a possible signal for subsequent degradation. Together, these results are consistent with a role of BLM in a replicative (S phase) and/or post-replicative (G2 phase) process. Oncogene (2000).

A murine ATFa-associated factor with transcriptional repressing activity.

The ATFa proteins, which are members of the CREB/ATF family of transcription factors, have previously been shown to interact with the adenovirus E1a oncoprotein and to mediate its transcriptional activity; they heterodimerize with Jun, Fos or related transcription factors, possibly altering their DNA-binding specificity; they also stably bind JNK2, a stress-induced protein kinase. Here we report the identification and characterization of a novel protein isolated in a yeast two-hybrid screen using the N-terminal half of ATFa as a bait. This 1306-residue protein (mAM, for mouse ATFa-associated Modulator) is rather acidic (pHi 4.5) and contains high proportions of Ser/Thr (21%) and Pro (11%) residues. It colocalizes and interacts with ATFa in mammalian cells, contains a bipartite nuclear localization signal and possesses an ATPase activity. Transfection experiments show that mAM is able to downregulate transcriptional activity, in an ATPase-independent manner. Our results indicate that mAM interacts with several components of the basal transcription machinery (TFIIE and TFIIH), including RNAPII itself. Together, these findings suggest that mAM may be involved in the fine-tuning of ATFa-regulated gene expression, by interfering with the assembly or stability of specific preinitiation transcription complexes.

ATM-dependent phosphorylation and accumulation of endogenous BLM protein in response to ionizing radiation.

Bloom's syndrome (BS), a rare genetic disease, arises through mutations in both alleles of the BLM gene which encodes a 3'-5' DNA helicase identified as a member of the RecQ family. BS patients exhibit a high predisposition to development of all types of cancer affecting the general population and BLM-deficient cells display a strong genetic instability. We recently showed that BLM protein expression is regulated during the cell cycle, accumulating to high levels in S phase, persisting in G2/M and sharply declining in G1, suggesting a possible implication of BLM in a replication (S phase) and/or post-replication (G2 phase) process. Here we show that, in response to ionizing radiation, BLM-deficient cells exhibit a normal p53 response as well as an intact G1/S cell cycle checkpoint, which indicates that ATM and p53 pathways are functional in BS cells. We also show that the BLM defect is associated with a partial escape of cells from the gamma-irradiation-induced G2/M cell cycle checkpoint. Finally, we present data demonstrating that, in response to ionizing radiation, BLM protein is phosphorylated and accumulates through an ATM-dependent pathway. Altogether, our data indicate that BLM participates in the cellular response to ionizing radiation by acting as an ATM kinase downstream effector.

The Krüppel-like core promoter binding protein gene is primarily expressed in placenta during mouse development.

The human core promoter binding protein (hCPBP) has been identified as a DNA-binding protein involved in the regulation of TATA box-less genes like those encoding the pregnancy-specific glycoproteins. Structurally, hCPBP contains three zinc fingers in the C-terminal domain, which is highly conserved in a number of proteins that constitute the Krüppel-like family of transcription factors. In the present work, we report the molecular cloning of the mouse CPBP (mCPBP) and its expression pattern during development as well as in adult tissues. The mouse cDNA encodes a protein of 283 amino acids that share 94.4% of identity with the hCPBP. The highest level of mCPBP transcript was detected in placenta, and its expression was lower in total embryos and in adult tissues. We also show by in situ hybridization that during embryonic development the mCPBP gene is mainly expressed in extra-embryonic structures throughout gestation; essentially no specific expression was detected in embryonic tissues. Our data demonstrate that CPBP transcript is enriched in the trophoblastic tissue and strongly suggest that its encoded polypeptide regulates target genes involved in placental development and pregnancy maintenance.

Role of the ATFa/JNK2 complex in Jun activation.

The ATFa proteins, which are members of the CREB/ATF family of transcription factors, display quite versatile properties. We have previously shown that they interact with the adenovirus E1a oncoprotein, mediating part of its transcriptional activity and heterodimerize with the Jun, Fos or related transcription factors, thereby modulating their DNA-binding specificity. In the present study, we report the sequence requirement of the N-terminal activation domain of ATFa and demonstrate the importance of specific threonine residues (Thr51 and Thr53) in addition to that of the metal-binding domain, in transcriptional activation processes. We also show that the N-terminal domain of ATFa which stably binds the Jun N-terminal kinase-2 (JNK2) (Bocco et al., 1996), is not a substrate for this kinase in vivo but, instead, serves as a JNK2-docking site for ATFa-associated partners like JunD, allowing them to be phosphorylated by the bound kinase.

Point mutations causing Bloom's syndrome abolish ATPase and DNA helicase activities of the BLM protein.

Bloom's syndrome (BS) is a rare human genetic disorder characterized by mutations within the BLM gene whose primary effects are excessive chromosome breakage and increased rates of sister chromatid interchange in somatic cells. We report the characterization of a murine protein (mBLM), highly related to the product of the human BLM gene. This protein exhibits an ATP-dependent DNA-helicase activity that unwinds DNA in a 3'-5' direction. Single amino acid substitutions found in BS cells, abolish both ATPase and helicase activities of this protein, indicating that defects in these BLM functions may be primarily responsible for BS establishment. These results provide the first evidence suggesting that the enzymatic activities of the BLM product are implicated in the upholding of genomic integrity.

Structure and expression of the ATFa gene.

The human ATFa proteins belong to the ATF/CREB family of transcription factors. We have previously shown that they mediate the transcriptional activation by the largest E1a protein and can heterodimerize with members of the Jun/Fos family. ATFa proteins have also been found tightly associated with JNK2, a stress-activated kinase. We now report on the structure of the ATFa gene, which mapped to chromosome 12 (band 12q13). Sequence analysis revealed that ATFa isoforms are generated by alternative splice donor site usage. A minimal promoter region of approximately 200 base pairs was identified that retained nearly full transcriptional activity. Binding sites for potential transcription factors were delineated within a GC-rich segment by DNase I footprinting. Expression studies revealed that ATFa accumulates in the nuclei of transfected cells, and the nuclear localization signal was defined next to the leucine zipper domain. As revealed by hybridization with mouse ATFa sequences, low levels of ATFa mRNAs were ubiquitously distributed in fetal or adult mice, with enhanced expression in particular tissues, like squamous epithelia and specific brain cell layers. The possible significance of coexpression of ATFa, ATF-2, and Jun at similar sites in the brain is discussed.

In vivo association of ATFa with JNK/SAP kinase activities.

The human ATFa proteins belong to the CREB/ATF family of transcription factors. We have previously shown that the ATFa proteins may contribute to the modulation of the transcriptional activity of the Jun/Fos complexes (Chatton et al. (1994). Oncogene, 9, 375-385). We now show that a protein kinase activity is strongly associated with ATFa in vivo, as revealed by coimmunoprecipitation of ATFa/kinase complexes from whole cell extracts, with antibodies against ATFa. Two independent regions were found to be implicated in kinase binding: a major interaction site is located within the N-terminal 82 residues comprising an important metal-chelating element; a weaker binding site corresponds to the basic sequence element preceding the C-terminal leucine-zipper of ATFa. Induction experiments suggest that each of these ATFa domains may interact with different kinases. The major activity is associated with the ATFa N-terminal domain. Based on its response to various inducers, on both in vitro and in vivo binding assays, and on its immunological properties, this activity most likely corresponds to the 54/55 kDa JNK2 protein. Taken together, these observations suggest that the ATFa proteins, among other CREB/ATF proteins, may be important effectors of cell signalling pathways.

Eukaryotic GST fusion vector for the study of protein-protein associations in vivo: application to interaction of ATFa with Jun and Fos.

We describe a multipurpose eukaryotic expression vector that incorporates the following features: restriction sites for in-frame insertion of cDNAs of interest between sequences encoding the glutathione-S-transferase (GST) and an oligohistidine element, allowing expression of the corresponding fusion proteins; a phosphorylation site for protein kinase A for in vitro labeling of the fusion protein; a T7 promoter for in vitro transcription and subsequent translation; and signals for single-stranded DNA production in bacteria. We have used this vector to demonstrate the formation in vivo of complexes between the transcription factor ATFa, a member of the family of ATF/CRE binding proteins, and the c-Jun or c-Fos proteins. Such interactions could be detected in crude extracts from cells transfected with vectors expressing the GST-ATFa fusion protein, as well as the c-Jun or c-Fos proteins. Complexes containing both ATFa and either c-Jun or c-Fos were specifically retained on glutathione (GSH)-agarose beads as revealed by immunoblot analyses. We also show that the leucine zipper domain of ATFa is essential for this interaction.

Identification of a second ATF/CREB-like element in the herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) promoter.

The herpes simplex virus type-1 (HSV-1) latency-associated transcript (LAT) promoter (LP) has been shown to function in a cell type-specific manner. We have constructed an extensive series of PCR deletion mutations of the LP from nucleotides +1 to -348 to delineate the specific sequences involved in the cell type-specific activity of the HSV-1 LP. This series of 5' LP deletion constructs has been transiently transfected into both C1300 (neuronal) and L929 (nonneuronal) cells. When nucleotides -75 to -83 were added to nucleotides +1 to -74, a three- to fourfold C1300-specific increase in promoter activity was observed. In addition, when sequences upstream of nucleotide -211 were added to nucleotides +1 to -211, a second threefold increase in promoter activity was observed in C1300 cells. To begin to understand the biochemical basis for these observations, we have examined the interaction of a segment of the HSV-1 LP (nucleotides -54 to -134) with factors present in neuronal and nonneuronal nuclear extracts. This region of the LP contains the sequence most proximal to the transcriptional start site demonstrated to be involved in cell type-specificity (nucleotides -75 to -83). By coupling the functional studies with electrophoretic mobility shift (EMS), oligonucleotide competition EMS, and antibody supershift EMS analyses, we have demonstrated that members of the activating transcription factor (ATF)/cyclic-AMP response element binding protein (CREB) transcription factor family interact with nucleotides -75 to -83 of the HSV-1 LP. The identification of a novel ATF/CREB-like element in the HSV-1 LP may facilitate the understanding of neuronal factors which regulate LAT expression during HSV-1 infection. These studies may ultimately provide additional insight concerning the role of HSV-1 LAT in the regulation of viral latency and reactivation.

Jun and Fos heterodimerize with ATFa, a member of the ATF/CREB family and modulate its transcriptional activity.

Three related clones encoding proteins (ATFa1, 2 and 3) with specific ATF/CRE DNA-binding activities have been isolated from HeLa cell cDNA libraries. All three isoforms have weak effects on the basal activity of the adenovirus E2a promoter. We present evidence suggesting that a C-terminal element of the ATFa molecules negatively interferes with the intrinsic activation function of these proteins. We also show that coexpression of ATFa with c-Jun, Jun-B or Jun-D stimulates ATFa-dependent reporter activity, while coexpression of c-Fos has no effect. Deletion analyses indicate that the metal-binding region of ATFa is dispensible for this effect, but that the domain comprising the leucine-zipper region of ATFa is required. Reciprocal co-immunoprecipitation experiments and electrophoretic band-shift assays with in vitro synthesized proteins reveal direct interactions between ATFa and Jun or Fos. The ATFa/c-Jun heterodimers, but not the ATFa/c-Fos complexes, bind efficiently to ATF, CRE or AP1 sites. The detection of ATFa-Jun complexes in crude extracts from HeLa cells transfected with ATFa and c-Jun expression vectors suggests that such ATFa/c-Jun heterodimers also form in vivo. Altogether these results indicate that the ATFa proteins may contribute to the modulation of the activity of the Jun/Fos complexes by altering their DNA-binding and transcriptional properties.

Rb may act as a transcriptional co-activator in undifferentiated F9 cells.

The reversible interaction of the retinoblastoma susceptibility gene product (Rb) with the cellular transcription factor E2F has recently been demonstrated. Activation of the adenovirus E2a promoter by the products of the viral E1a gene correlates with the ability of both early E1a proteins to sequester Rb, thereby releasing E2F from inactive complexes with this protein. The E2a promoter is also efficiently stimulated by a product (17.5 kDa) of the viral E4 gene. The specific interaction of this E4 protein with E2F results in the formation of complexes that bind cooperatively to the two neighboring E2F binding sites in the E2a promoter. We have previously shown that in undifferentiated F9 cells (F9EC) the E2a promoter is refractory to E2F-mediated activation by E1a, but not by E4. Using both band-shift and transfection experiments, we now demonstrate (i) that in F9EC cells the E4 product, in combination with E2F, recruits Rb into a stable multiprotein complex and (ii) that in these undifferentiated cells, as opposed to their differentiated counterpart, Rb is actively involved in the transcriptional stimulation of the E2a promoter by E4. Our results suggest that, depending on the cell state, Rb may behave either as a transcriptional activator (F9EC cells) or as a transcriptional inhibitor (differentiated F9 cells).

Transcriptional activation by the adenovirus larger E1a product is mediated by members of the cellular transcription factor ATF family which can directly associate with E1a.

We recently isolated three cDNA clones encoding closely related proteins (ATFa1, ATFa2, and ATFa3) that belong to the activating transcription factor-cyclic AMP-responsive element family of cellular transcription factors. Using cotransfection experiments, we showed that these proteins mediate the transcriptional activation induced by the adenovirus E1a 13S mRNA gene product and that the zinc-binding domains present in both E1a conserved region 3 and the most N-terminal portion of the ATFa proteins play crucial roles in this activity. Reciprocal coimmunoprecipitation experiments demonstrated direct interactions between these proteins. Neither the conserved region 3 domain of E1a nor the N-terminal metal-binding element of ATFa is essential for these interactions. The simultaneous alteration of both the N-terminal and the C-terminal domains of ATFa abolished E1a binding, while either mutation alone failed to impair these interactions.

Isolation and characterization of two novel, closely related ATF cDNA clones from HeLa cells.

ATF or CRE binding proteins are cellular transcription factors involved in the regulation of adenovirus Ela-responsive and cellular cAMP-inducible promoters. We report the isolation from a HeLa cell cDNA library of two clones that encode proteins with specific ATF/CRE DNA binding activity. The two clones differ by a 63 bp element which is retained in one (ATF-a) and deleted from the other (ATF-a delta) and which may correspond to an alternative exon. The peptide sequences (483 and 462 amino acids, respectively) derived from each of these cDNAs are identical, except for the additional 21 amino acids in ATF-a, but clearly differ from the other ATF/CREB proteins reported. All of them, however, share a conserved leucine zipper domain also found in other transcription factors. ATF-a and ATF-a delta therefore represent two closely related members of a larger multigene family of proteins that interact with conserved promoter elements.

Stereoalignment requirements for activation of transcription by the simian virus 40 enhancer.

We investigated the contribution to the enhancer activity of protein-protein interactions between specific trans-acting factors bound to neighbouring sequence elements of the SV40 early enhancer-promoter region. To this end, we altered the distance between the SV40 enhancer-promoter elements by inserting systematically increasing lengths of spacer DNA. We show here that the level of transcription from the SV40 early promoter decreases with the spacing between enhancer and promoter regions. In the case of insertions shorter than 125 bp, the promoter activity exhibits a strong dependence of insertion lengths of multiples of about 10 bp. This periodic effect is no longer observed for layer insertions, reflecting the torsional flexibility of DNA. These data provide evidence that, between promoter and/or enhancer elements, periodic interactions of transcriptional nucleoprotein complexes exist and stereospecific alignments are necessary to obtain an efficient initiation of transcription from the SV40 early promoter.

Negative and positive factors determine the activity of the polyoma virus enhancer alpha domain in undifferentiated and differentiated cell types.

The host range of polyoma virus is dependent upon the activity of its enhancer, which is inactive in undifferentiated embryonal carcinoma cells, such as F9 cells, and is active after their differentiation. We show here that the activity of the alpha domain of the polyoma virus enhancer displays a similar cell-specificity and inducibility as does the whole enhancer. We present evidence to show that its activity is determined by the balance between the activities of two factors, PEA2, a labile repressor, and PEA1, an inducible positive factor that we have characterized previously. Changes in repressor activity help account for the increase in alpha-domain activity after differentiation of F9 cells. These results suggest that PEA2 is crucial in the regulation of viral gene expression and perhaps more generally in the control of gene expression during differentiation.

A Harvey-ras responsive transcription element is also responsive to a tumour-promoter and to serum.

The ras oncogenes are implicated in the onset of some human tumours, and in cellular proliferation and terminal differentiation. The ras proteins are plasma membrane bound transducers of signals between the outside of the cell and unknown targets in the cell. Identifying these targets and understanding how they are regulated will have a major impact on our understanding of the molecular basis of transformation. We have already shown that c-Ha-ras and the tumor promoter TPA (12-o-tetradecanoyl phorbol-13-acetate) can activate a transcriptional enhancer. We now report the identification of a short sequence in the polyoma virus (Py) enhancer which mediates Ha-ras activation, and show that this sequence (ras responsive element, RRE) also mediates activation by TPA and serum. This responsive element is a specific binding-site for the mouse transcription factor PEA1 (ref. 4 and below) and for the jun oncogene (ref. 5 and M. Karin, personal communication). These results are in keeping with a role for ras protein in signal transduction from outside the cell to a transcription factor in the nucleus, through protein kinase C. The striking similarity between RRE and DNA sequences present in the promoter regions of a number of transformation-related genes suggests that deregulated activation of RRE is a critical event in transformation.

The yeast VAS1 gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases.

S1 mapping on the VAS1 structural gene indicates the existence of two classes of transcripts initiating at distinct in-frame translation start codons. The longer class of VAS1 transcripts initiates upstream of both ATG codons located 138 base pairs away and the shorter class downstream of the first ATG. A mutation that destroys the first AUG on the long message results in respiratory deficiency but does not affect viability. Mutation of the ATG at position 139 leads to lethality because the initiating methionine codon of the essential cytoplasmic valyl-tRNA synthetase has been destroyed. N-terminal protein sequence data further confirm translation initiation at ATG-139 for the cytoplasmic valyl-tRNA synthetase. From these results, we conclude that the VAS1 single gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases. The presequence of the mitochondrial valyl-tRNA synthetase shows amino acid composition but not the amphiphilic character of imported mitochondrial proteins. From mutagenesis of the ATG-139 we conclude that the presequence specifically targets the cytoplasmically synthesized mitochondrial valyl-tRNA synthetase to the mitochondrial outer membrane and prevents binding of the enzyme core to cytoplasmic tRNAVal.