Shut-off of actin biosynthesis in adenovirus serotype-2-infected cells

Adenovirus produces a dramatic shut-off of host protein synthesis after infection of HeLa cells. The level of actin messenger RNAs remained relatively unchanged after viral infection, when assayed by in vitro translation and two-dimensional gel electrophoresis analysis of the proteins or hybridization of the total cytoplasmic RNAs to the human actin gene. The distribution of actin mRNA in the polyribosomes is altered after adenovirus infection, with small polyribosomes and monoribosomes of the infected cells occupied by actin messages untranslatable in a rabbit reticulocyte lysate. The large polyribosomes still retain enough functional mRNAs to provide significant levels of actin protein in a rabbit reticulocyte in vitro translation system. In contrast, in homologous infected cell lysates, the translation of exogenous actin mRNA is greatly reduced when compared to uninfected HeLa cell lysates. In nuclease-treated uninfected or infected HeLa cell-free extracts, translation of viral mRNA is equally efficient and higher than that of actin mRNA. Thus, translational regulatory mechanisms which include inactivation of a part of the actin mRNA population accompanied by displacement to small polysomes and/or virus-induced modification of the cellular translational machinery to discriminate against cellular actin mRNA seem to account for the sharp reduction in actin protein synthesis of adenovirus-infected cells.     

Comparison of the structure and DNA-binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus

Human papillomaviruses (HPVS) that infect the genital tract can be divided into two groups: high-risk HPV types, such as HPV 16 and HPV 18, are associated with cancer, low-risk HPV types, such as HPV 6, are associated with benign warts. In both high-risk and low-risk HPV types, the papillomavirus E2 protein binds to four sites within the viral long control region (LCR) and regulates viral gene expression. Here, we present the crystal structure of the minimal DNA-binding domain (DBD) from the HPV 6 E2 protein. We show that the HPV 6 E2 DBD is structurally more similar to the HPV 18 and bovine papillomavirus type 1 (BPV1) E2 proteins than it is to the HPV 16 E2 protein. Using gel retardation assays, we show that the hierarchy of E2 sites within the HPV 16 and HPV 6 LCRs are different. However, despite these differences in structure and site preference, both the HPV 16 and 6 E2 DBDs recognise an extended version of the consensus E2 binding site derived from studies of the BPV1 E2 protein. In both cases, the preferred binding site is 5'AACCGN(4)CGGTT3', where the additional flanking base-pairs are in bold and N(4) represents a four base-pair central spacer. Both of these HPV proteins bind preferentially to E2 sites that contain an A:T-rich central spacer. We show that the preference for an A:T-rich central spacer is due, at least in part, to the need to adopt a DNA conformation that facilitates protein contacts with the flanking base-pairs.     

Effect of aphidicolin on the elongation step of adenovirus DNA replication in vitro

Adenovirus DNA synthesis carried out in vitro was inhibited by the aphidicolin. However, 30% of the DNA synthesis was resistant to aphidicolin even at a concentration of 200 micrograms/ml. When the distribution patterns of the radioactivity of the products synthesized in the presence of 50 micrograms/ml of the drug was examined after HindIII digestion of the product DNA, the radioactivity appeared preferentially in the fragments mapping nearest to the ends of the molecule. Pulse-chase experiment showed that the terminal fragments were synthesized with or without aphidicolin but that in the presence of aphidicolin the rate of elongation rapidly slowed down beyond this region, suggesting that a DNA polymerase sensitive to aphidicolin may participate in the synthesis of the internal region of adenovirus DNA.     

Polypyrimidine tract binding protein inhibits IgM pre-mRNA splicing by diverting U2 snRNA base-pairing away from the branch point

The mouse immunoglobulin (IgM) pre-mRNA contains a splicing inhibitor that bears multiple binding sites for the splicing repressor polypyrimidine tract binding protein (PTB). Here we show that the inhibitor directs assembly of an ATP-dependent complex that contains PTB and U1 and U2 small nuclear RNAs (snRNAs). Unexpectedly, although U2 snRNA is present in the inhibitor complex, it is not base-paired to the branch point. We present evidence that inhibitor-bound PTB contacts U2 snRNA to promote base-pairing to an adjacent branch point–like sequence within the inhibitor, thereby preventing the U2 snRNA–branch point interaction and resulting in splicing repression. Our studies reveal a novel mechanism by which PTB represses splicing.     

A comparison of the DNA binding properties of histone-like proteins derived from representatives of the two kingdoms of the Archaea

Abstract The nucleoid protein composition, the enhancement of DNA electrophoretic mobility, the toroidal wrapping and the helical period of DNA complexed with nucleoid proteins from species within the archaeal kingdom Euryarchaeota was shown to contrast with the composition and properties of nucleoid proteins from Sulfolobus solfataricus , a member of the archaeal kingdom Crenarchaeota. This result was seen to support the hypothesis that archaeal histones with homology to the eukaryal hi stone consensus are a diagnostic feature of the Euryarchaeota.     

The nucleotide sequence of the polypeptide IX gene of human adenovirus type 3

The nucleotide sequence of the DNA segment encompassing the polypeptide IX gene of class B human adeno-virus serotype 3 (Ad3) has been determined using cloned restriction fragments. There is only a single, open translational reading frame capable of specifying a protein of 138 amino acids, comparable to the M_r 12000–13000 of protein IX detected in virions (Wadell, 1980). The corresponding region of a closely related class B virus, Ad7, is virtually identical (Dijkema et al., 1981), but the comparable segments of class C viruses Ad2 or Ad5 are much less homologous (Aleström et al., 1980; Maat et al., 1980). There are 150 single bp changes and 19 deletion-insertions, at least one frameshift, together affecting 210 nucleotides within the 455 bp comparison positions of the protein-coding regions of Ad2 (423 bp) and Ad3 (417 bp). Each of the 19 deletion-insertions involves an integral multiple of 3 bp in phase with the open translation frame. There is no “TATA” promoter box in Ad3 DNA at the position comparable to that of Ad2. The deduced protein sequences near the amino-terminus are extensively conserved between the two classes of viruses, but the carboxy-terminal portion and the nucleotide sequences flanking the gene are much more diverged. In both classes, these N- and C-terminal regions of the inferred proteins are linked by an alanine-rich chain, an arrangement suggestive of two functional domains.     

Construction of restriction enzyme fragment libraries containing DNA from human adenovirus types 2 and 5

Restriction-fragment libraries containing adenovirus type 2 (Ad2) DNA have been constructed, using the pBR322 plasmid (Bolivar et al., 1977) as a vector. Clones have been isolated which contain all the HindIII fragments of Ad2 DNA except the terminal G- and K-fragments inserted into the HindIII cleavage site of the vector. All the 13 SmaI-fragments of Ad2 DNA were separately inserted into the PstI site of the pBR322 vector after addition of homopolymeric poly(dG) tails to the fragments and poly(dC) tails to the linearized plasmid. Two large fragments of adenovirus type 5 (AD5) DNA, located between map positions 17.0 and 59.5 and between map positions 59.5 and 97.3, respectively, were cloned using bacteriophage lambda as a vector. All clones, which are described in the present report, are available upon request.     

The effect of 2′-fluoro-2′-deoxycytidine on herpes virus growth

The effect of 2′-fluoro-2′-deoxycytidine (dCfl) on the growth of certain viruses of the herpes type was investigated. It is shown that the compound has considerable anti-viral activity against HSV-I, HSV-II, pseudorabies virus and equine abortion virus. It has an effect comparable to that of araC and is more efficient than br⁵dC, but less so than acyclovir. Experiments with thymidine kinase-negative strains of HSV-I indicated that dCfl was phosphorylated by the viral kinase, and its K_m appears to be low and close to that of thymidine. Density gradient centrifugation enabled us to show that dCfl was incorporated into cellular and viral DNA and RNA. The cytotoxic activity of dCfl appears to be about 10-times smaller than that of araC. Removal of the nucleoside analog, washing and replacement with deoxycytidine reversed this effect, indicating rather a cytostatic than cytotoxic effect.     

Human DDB2 splicing variants are dominant negative inhibitors of UV-damaged DNA repair

Damaged DNA-binding protein (DDB) is a heterodimer (DDB1 and DDB2), which is implicated in the repair of UV-irradiated DNA damage. Here we have identified four DDB2 variants from HeLa cells (D1-D4) that are generated by alternative splicing. Analysis of tissue distribution by RT-PCR indicates that D1 is the most highly expressed in human brain and heart. A DNA repair assay revealed that both D1 and D2 are dominant negative inhibitors. Electrophoresis mobility shift assays indicated that D1 and D2 are not part of the damaged DNA-protein complex. Co-immunoprecipitation studies show that DDB2-WT interacts with D1 and itself. Nuclear import of DDB1 was less induced by transfection with D1 than WT. Based on these results, D1 and D2 are dominant negative inhibitors of DNA repair, which is probably due to disruption of complex formation between DDB1 and DDB2-WT and of DDB1 nuclear import.     

A complex composed of at least two HeLa nuclear proteins protects preferentially one DNA strand of the simple (gt)n(ga)m containing region of intron 2 in HLA-DRB-genes

Electrophoretic mobility shift assays reveal that HeLa neuclear proteins bind fast and with measurable affinity to target DNAs containing mixed simple repetitive (gt)_n(ga)_m stretches. Preincubation of the proteins at elevated temperature prevents the formation of the major DNA/protein complex in favour of several distinct assemblies. A similar pattern of retarded bands was observed employing higher salt concentrations in binding reaction. Thus conformational changes of different proteins appear to influence the complex rather than alternating DNA structures. Separation of the total nuclear extract into a water soluble and an insoluble protein fraction leads to a complete loss of target DNA bindinlg capability of the fractions. The binding capacity is restored by combining the two fractions suggesting that at least two protein components are necessary to form a complex with the target sequence. The proteins can be differentiated into head sensitive, water soluble and temporary stable, water insoluble, respectively. Furthermore, specifically binding polypeptides are not detectable by Southwestern analyses, probably because the essential components are separated during electrophoresis. DNase 1 footpoint analyses yield four different protein binding regions only on the (gt)_n(ga)_m harbouring strand. The footprints cover larger portions of the mixed simple repeat in addition to a portion 5′ of the (gt)_n part. Hence at lealst two nuclear protein components of unknown biological function have to be present simultaneously to protect preferentially the (gt)_n(ga)_m-containing strand intron 2 in HLA-DRB genes     

Composition and DNA-binding properties of the nuclear matrix proteins from mammalian cell nuclei

A rapidly sedimenting DNA-protein complex was isolated from nuclear lysates in 2 M NaCl and characterized with regard to its polypeptide composition and the DNA-binding properties of the purified proteins. The complex consists of the nuclear matrix with attached DNA. Electrophoresis in SDS-polyacrylamide gels revealed two major and five minor polypeptide bands, mainly in the 60 to 75 kDa molecular weight region. The DNA-matrix complex dissociated into free DNA and proteins in the presence of 2 M NaCl and 5 M urea. The proteins could be purified by chromatography on hydroxyapatite and showed a strong tendency to reassociate at 0.15 M NaCl concentration in the absence of urea. DNA was bound to the reassociated proteins at 0.15 M NaCl concentration. Part of the DNA-protein complex was stable at 1 M NaCl concentration. The binding appeared to be random with regard to the DNA sequence.     

Fusion and Fission, the Evolution of Sterol Carrier Protein-2

Sterol carrier protein-2 (SCP-2) is an intracellular, small, basic protein domain that in vitro enhances the transfer of lipids between membranes. It is expressed in bacteria, archaea, and eukaryotes. There are five human genes, HSD17B4, SCPX, HSDL2 STOML1, and C20orf79, which encode SCP-2. HSD17B4, SCPX, HSDL2, and STOML1 encode fusion proteins with SCP-2 downstream of another protein domain, whereas C20orf79 encodes an unfused SCP-2. We have extracted SCP-2 domains from databases and analyzed the evolution of the eukaryotic SCP-2. We show that SCPX and HSDL2 are present in most animals from Cnidaria to Chordata. STOML1 are present in nematodes and more advanced animals. HSD17B4 which encodes a D-bifunctional protein (DBP) with domains for D-3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase, and SCP-2 are found in animals from insects to mammals and also in fungi. Nematodes, amoebas, ciliates, apicomplexans, and oomycetes express an alternative DBP with the SCP-2 domain directly connected to the D-3-hydroxyacyl-CoA dehydrogenase. This fusion has not been retained in plant genomes, which solely express unfused SCP-2 domains. Proteins carrying unfused SCP-2 domains are also encoded in bacteria, archaea, ciliates, fungi, insects, nematodes, and vertebrates. Our results indicate that the fusion between D-3-hydroxyacyl-CoA dehydrogenase and SCP-2 was formed early during eukaryotic evolution. There have since been several gene fission events where genes encoding unfused SCP-2 domains have been formed, as well as gene fusion events placing the SCP-2 domain in novel protein domain contexts. [Reviewing Editor: Dr. Brian R. Morton]     

Thermostability, oligomerization and DNA-binding properties of the regulatory protein ArgR from the hyperthermophilic bacterium Thermotoga neapolitana

The hexameric regulatory protein ArgR formed by arginine-mediated dimerization of identical trimers governs the expression of genes required for arginine metabolism and some other genes in mesophilic and moderately thermophilic bacteria. We have cloned the argR gene from two hyperthermophilic bacteria of the genus Thermotoga. The two-domain ArgR proteins encoded by T. neapolitana and T. maritima share a low degree of sequence similarity with other bacterial arginine repressors. The ArgR protein from T. neapolitana binds to an operator located just upstream of its coding sequence and, therefore, the argR gene may be autoregulated. The protein has extremely high intrinsic thermostability and tolerance to urea. Moreover, its binding to target DNA increases the melting temperature by approximately 15° C. The formation of oligomeric ArgR-DNA complexes is a function of protein concentration, with hexameric complexes being favoured at higher concentrations. In the presence of arginine the hyperthermophilic ArgR protein binds to its own operator, argRo, only by forming hexamer ArgR-DNA complexes, whereas both trimer-DNA and hexamer-DNA complexes are detected in the absence of arginine. However, the affinity of T. neapolitana ArgR for DNA has been found to be higher for a mixture of trimers and non-bound hexamers than for arginine-bound hexamers. Our data indicate that genes for arginine biosynthesis are clustered in a putative operon, which could also be regulated by the ArgR protein, in the hyperthermophilic host. Received: 19 July 1999 / Accepted: 4 November 1999