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T Shenk

Publications and source records attributed to T Shenk.

At least 91 records · Page 5Linked to original sources
PubMed1991

A 32-kilodalton protein binds to AU-rich domains in the 3' untranslated regions of rapidly degraded mRNAs.

An AU-rich sequence present within the 3' untranslated region has been shown to mark some short-lived mRNAs for rapid degradation. We demonstrate by label transfer and gel shift experiments that a 32-kDa polypeptide, present in nuclear extracts, specifically interacts with the AU-rich domains present within the 3' untranslated region of human granulocyte-macrophage colony-stimulating factor, c-fos, and c-myc mRNAs and a similar domain downstream of the poly(A) addition site of the adenovirus IVa2 mRNA. Competition experiments and partial protease analysis indicated that the same polypeptide interacts with all four RNAs. A single AUUUA sequence in a U-rich context was sufficient to signal binding of the 32-kDa polypeptide. Insertion of three copies of this minimal recognition site led to markedly reduced accumulation of beta-globin RNA, while the same insert carrying a series of U-to-G changes had little effect on RNA levels. Steady-state levels of beta-globin-specific nuclear RNA, including incompletely processed RNA, and cytoplasmic mRNA were reduced. Cytoplasmic mRNA containing the AU-rich recognition sites for the 32-kDa polypeptide exhibited a half-life shorter than that of mRNA with a mutated insert. We suggest that binding of the 32-kDa polypeptide may be involved in the regulation of mRNA half-life.

Adenine↗
PubMed1990

Transcription of adenovirus and HeLa cell genes in the presence of drugs that inhibit topoisomerase I and II function.

The requirements for topoisomerases in transcription of adenovirus and HeLa cell genes were analyzed using drugs that specifically inhibit either topoisomerases I or II. Cleavage of viral DNA by topoisomerases in the presence of either camptothecin or VM26 was used to determine drug concentrations that led to maximal inhibition of ligation in the cleavage and ligation step of topoisomerase I or II respectively. Inhibition of topoisomerase II with VM26 did not cause a direct reduction in transcription of adenoviral genes or HeLa cell heat shock genes. VM26 did, however, interfere with other cellular processes. It reduced nucleoside uptake into HeLa cells from the medium, and it altered the normal nuclear to cytoplasmic ratio of specific RNAs. Treatment of cells with camptothecin to inhibit topoisomerase I reduced but did not abolish transcription of viral and HeLa cell genes. Transcription mediated by both RNA polymerases I and II was reduced. Topoisomerase II did not appear to substitute for topoisomerase I in transcription since treatment of cells with VM26 and camptothecin did not reduce transcript accumulation relative to cells treated with camptothecin alone.

Adenovirus Early Proteins↗
PubMed1990

A multisubunit factor, CstF, is required for polyadenylation of mammalian pre-mRNAs.

We have purified and characterized a factor required for accurate polyadenylation of mammalian pre-mRNAs in vitro. This factor, called cleavage-stimulation factor (CstF), is composed of three distinct polypeptide subunits of 77, 64, and 50 kD. Using monoclonal antibodies directed against the 64- and 50-kD subunits, we show that CstF is required for efficient cleavage of polyadenylation substrates. Furthermore, CstF present in unfractionated nuclear extracts interacts with pre-mRNAs containing the signal sequence AAUAAA, but not AAGAAA, in such a manner that the 64-kD subunit can be cross-linked to the RNA by UV light. This polypeptide is thus identical to the previously described 64-kD nuclear protein that binds to AAUAAA-containing RNAs. Finally, indirect immunofluorescence of fixed cells indicates that CstF is distributed diffusely throughout the nucleus in a granular pattern distinct from the "speckled" pattern displayed by factors involved in pre-mRNA splicing, but similar to that of heterogeneous nuclear ribonucleoproteins. A model is presented in which CstF binds specifically to nascent RNA polymerase II transcripts and, by interacting with other factors, results in a rapid initiation of 3'-end processing of pre-mRNAs.

Antibodies, Monoclonal↗
PubMed1990

Adenovirus terminal protein mediates both nuclear matrix association and efficient transcription of adenovirus DNA.

Adenovirus DNA is tightly bound to the nuclear matrix throughout the course of infection. Analysis of adenovirus DNA from infected HeLa cell nuclei after extraction with lithium diiodosalicylate and digestion with restriction enzymes demonstrated that the sites of tightest attachment occur in the terminal fragments of the linear viral chromosome. Analysis of viruses mutated in the precursor terminal protein coding sequence demonstrated that the terminal protein, which is covalently attached to the 5' end of each DNA strand, mediates the tight binding. Virions containing chromosomes with mutant terminal proteins were unpackaged and viral DNA accumulated in the nucleus at a normal rate and competed for the limiting component during transcription complex formation, but their early genes were transcribed at reduced efficiency by both RNA polymerases II and III. The transcriptional defects were not complemented by coinfection with a wild-type virus. We propose that the adenovirus chromosome may exist as a single chromatin domain during infection and that binding of DNA to the nuclear matrix may play a critical role in adenovirus transcription.

Adenoviruses, Human↗
PubMed1990

Topoisomerase I and II cleavage of adenovirus DNA in vivo: both topoisomerase activities appear to be required for adenovirus DNA replication.

Sites of topoisomerase I and II cleavage across large portions of the adenovirus type 5 genome were mapped by using the drugs camptothecin and VM26, respectively. These drugs prolong the half-lives of the covalent DNA-protein intermediates in which the DNA is transiently cleaved, and so treatment with protein denaturants after exposure to the drugs leads to DNA strand scission at the site of topoisomerase cleavage. Strong topoisomerase II cleavage sites occurred in clusters throughout the regions examined, including both transcribed regions and transcriptional control regions. The efficiency of topoisomerase II cleavage increased as the rate of adenovirus DNA replication increased and then decreased with the decreasing rate of replication late in the infection cycle. The increase was not dependent on expression of the E1A gene, whose products activate transcription of the early viral genes. Positions of topoisomerase II cleavage sites did not vary during the infection. Topoisomerase I cleavage sites were also found throughout the examined regions, with the strongest sites occurring near the ends of the transcription units. Topoisomerase I cleavage in the E1 region occurred much more frequently than topoisomerase II cleavage, was not dependent on E1A gene expression, and remained at a similar level from the early viral phase into the late viral phase. Treatment of infected cells with either drug prevented efficient replication of adenovirus DNA. Inhibition of topoisomerase I activity led to an immediate cessation of adenovirus DNA replication, while inhibition of topoisomerase II blocked replication only after completion of approximately one additional round.

Adenovirus Early Proteins↗
PubMed1990

The adenovirus type 5 i-leader open reading frame functions in cis to reduce the half-life of L1 mRNAs.

The 440-nucleotide adenovirus type 5 i-leader sequence, encoding a 13.6-kilodalton protein, is located between the second and third components of the tripartite leader sequence. It appears primarily on the L1 family of mRNAs. To study its function, we constructed two point mutations within the i leader. pm382 lacks the wild-type i-leader splice acceptor and failed to splice the leader onto L1 mRNAs. pm383 lacks the ATG used for translation of the i-leader protein; it synthesized i-leader-containing mRNAs, but failed to produce detectable levels of the polypeptide. Both mutants exhibited modestly reduced yields in some but not all cell lines tested and accumulated slightly elevated levels of L1 mRNA and L1 52- and 55-kilodalton proteins in infected cells. Mutant phenotypes were consistently more pronounced in pm382- than in pm383-infected cells. In wild-type virus-infected cells, L1 mRNAs lacking the i leader displayed a half-life of about 26 h, whereas L1 mRNAs containing the leader were much less stable, with a half-life of less than 4 h. In pm383-infected cells (ATG mutant), L1 mRNAs containing the i leader exhibited a half-life of 26 h. The abnormally long half-life of pm383-encoded L1 mRNAs containing a mutant i leader was not reduced by coinfection with wild-type virus, suggesting that synthesis of the i-leader protein leads to destabilization of the i-leader-containing L1 mRNA undergoing translation.

Adenoviruses, Human↗
PubMed1990

The adenovirus DNA-binding protein stimulates the rate of transcription directed by adenovirus and adeno-associated virus promoters.

The DNA-binding protein (DBP) encoded by the E2A region of adenovirus type 5 was found to enhance the expression of a reporter gene controlled by several different promoters within transfected cells. The rate of synthesis of correctly initiated transcripts was increased by the DBP. The adeno-associated virus P5 promoter and the adenovirus E1A and E2A early and major late promoters responded to the DBP by increases in expression ranging from 6- to 27-fold, while the adenovirus E4 promoter was slightly inhibited by DBP. The adenovirus major late promoter showed a greater response to DBP than to the E1A transactivator protein, suggesting that the DBP plays a central role in activation of the late promoter.

Adenovirus Early Proteins↗
PubMed1990

The adenovirus E4 17-kilodalton protein complexes with the cellular transcription factor E2F, altering its DNA-binding properties and stimulating E1A-independent accumulation of E2 mRNA.

E2F is a cellular DNA-binding factor. Its binding activity is changed within adenovirus-infected cells so that it binds cooperatively to pairs of properly spaced and oriented E2F recognition sites. In the work described in this report, the conversion to cooperative binding was shown to require the adenovirus E4 17-kilodalton (kDa) polypeptide. Mutant viruses carrying alterations within the E4 17-kDa coding region failed to generate the infection-specific, cooperatively binding form of E2F. It was possible to alter E2F from uninfected cells so that it bound cooperatively by incubation with a partially purified fraction obtained from infected cells. The E4 17-kDa protein copurified with this activity and was also found to be present in a complex containing E2F. Consistent with its ability to alter the binding of E2F to its recognition sites within the E2 promoter, the E4 17-kDa polypeptide contributed to maximal expression of E2 mRNAs in some cell types. Its ability to enhance E2 transcription did not require expression of the E1A transactivator protein. These results are consistent with a model which proposes that the E4 17-kDa polypeptide binds to the cellular E2F factor, altering its binding behavior and thereby enhancing its ability to stimulate transcription.

Adenovirus Early Proteins↗
PubMed1990

A uridylate tract mediates efficient heterogeneous nuclear ribonucleoprotein C protein-RNA cross-linking and functionally substitutes for the downstream element of the polyadenylation signal.

Every RNA added to an in vitro polyadenylation extract became stably associated with both the heterogeneous nuclear ribonucleoprotein (hnRNP) A and C proteins, as assayed by immunoprecipitation analysis using specific monoclonal antibodies. UV-cross-linking analysis, however, which assays the specific spatial relationship of certain amino acids and RNA bases, indicated that the hnRNP C proteins, but not the A proteins, were associated with downstream sequences of the simian virus 40 late polyadenylation signal in a sequence-mediated manner. A tract of five consecutive uridylate residues was required for this interaction. The insertion of a five-base U tract into a pGEM4 polylinker-derived transcript was sufficient to direct sequence-specific cross-linking of the C proteins to RNA. Finally, the five-base uridylate tract restored efficient in vitro processing to several independent poly(A) signals in which it substituted for downstream element sequences. The role of the downstream element in polyadenylation efficiency, therefore, may be mediated by sequence-directed alignment or phasing of an hnRNP complex.

Base Sequence↗
PubMed1990

A multicomponent complex is required for the AAUAAA-dependent cross-linking of a 64-kilodalton protein to polyadenylation substrates.

A 64-kilodalton (kDa) polypeptide that is cross-linked by UV light specifically to polyadenylation substrate RNAs containing a functional AAUAAA element has been identified previously. Fractionated HeLa nuclear components that can be combined to regenerate efficient and accurate polyadenylation in vitro have now been screened for the presence of the 64-kDa protein. None of the individual components contained an activity which could generate the 64-kDa species upon UV cross-linking in the presence of substrate RNA. It was necessary to mix two components, cleavage stimulation factor and specificity factor, to reconstitute 64-kDa protein-RNA cross-linking. The addition of cleavage factors to this mixture very efficiently reconstituted the AAUAAA-specific 64-kDa protein-RNA interaction. The 64-kDa protein, therefore, is present in highly purified, reconstituted polyadenylation reactions. However, it is necessary to form a multicomponent complex to efficiently cross-link the protein to a substrate RNA.

Base Sequence↗
PubMed1990

Conversion of the lac repressor into an allosterically regulated transcriptional activator for mammalian cells.

A novel mammalian regulatory system was created by using the Escherichia coli lac repressor. The lac repressor was converted into a mammalian transcriptional activator by modifying the lac repressor coding region to include a nuclear localization signal from the simian virus 40 (SV40) large tumor antigen and the transcription activation domain from the herpes simplex virus type 1 virion protein 16. The lac activator protein (LAP) fusions were potent activators of several promoters containing lac operator sequences positioned either upstream or downstream of the transcription unit. A single lac operator allowed for transactivation, whereas multiple operators acted synergistically when separated by a small distance. Promoters containing 14 or 21 operator sequences were induced at least 1,000-fold in response to LAP, reaching levels of activity 20 to 30 times greater than that of the SV40 early promoter in HeLa cells. Activation was strongly inhibited by isopropyl-beta-D-thiogalactoside (IPTG), indicating that LAP retained the functions needed for allosteric regulation. LAP was bifunctional, also acting as a repressor of expression of an SV40 promoter containing an operator immediately downstream of the TATA box. Finally, genetic selection schemes were developed such that LAP-expressing cell lines can be generated at high frequency from either established or primary cells in culture.

Allosteric Regulation↗
PubMed1989

Functional analysis of point mutations in the AAUAAA motif of the SV40 late polyadenylation signal.

We have constructed 14 independent point mutations in the conserved AAUAAA element of the SV40 late polyadenylation signal in order to study the recognition and function of alternative polyadenylation signals. A variant RNA containing an AUUAAA was polyadenylated at 20% the level of wild-type substrate RNA, while all other derivatives tested were not functional in vitro. The AUUAAA variant RNA formed specific complexes in native polyacrylamide gels and crosslinked to the AAUAAA-specific 64kd polypeptide, but at a lower efficiency than wild-type substrate RNA.

Base Sequence↗
PubMed1989

The adenovirus E1B 55 kd protein influences mRNA transport via an intranuclear effect on RNA metabolism.

The adenovirus type 5 early region 1B encodes a 55 kd polypeptide that functions after transcription and processing to facilitate cytoplasmic accumulation of late viral mRNAs during lytic infection. A virus, dl338, carrying a deletion within the coding region for the 55 kd product, was found to be cold-sensitive for growth. Accumulation of late viral mRNAs was more severely inhibited at 32 than at 37 degrees C in dl338-infected cells. The metabolism of late viral transcripts was analysed within the nucleus of dl338-infected cells at 32 degrees C. Late viral mRNAs failed to accumulate efficiently within a nuclear compartment defined by specific RNA extraction conditions. Normally, RNA accumulated within this operationally defined compartment after leaving the nuclear matrix and before associating with the nuclear envelope. These results indicate that the 55 kd polypeptide encoded by early region 1B facilitates an intranuclear step in the metabolism of viral mRNAs, resulting in improved transport of these RNAs to the cytoplasm.

Adenovirus Early Proteins↗
PubMed1989

C-terminal domain of the adenovirus E1A oncogene product is required for induction of cytotoxic T lymphocytes and tumor-specific transplantation immunity.

Adenovirus genes required for the elicitation of adenovirus group C-specific cytolytic T lymphocytes (CTLs) and for the induction of adenovirus-specific transplantation antigen (TSTA) were identified by immunization with a library of adenovirus mutants. The group C Ad-specific CTL response was elicited by immunization with wild-type adenovirus type 5 (Ad5) or with recombinant adenoviruses containing Ad5 E1A gene. The specific CTL response was also elicited by Ad5 virus constructs which express only the 12 S or 13 S E1A early mRNA, but not with viruses unable to express E1A protein sequences normally encoded by the E1A early messages. The induction of transplantation immunity against tumorigenic Ad-transformed cells was studied next. The product encoded by either 13 S and 12 S E1A mRNA alone was sufficient for strong TSTA activity. A series of viruses with mutations within the first exon of the E1A message also induced strong TSTA, while Ad5 mutants with lesions within the second exon failed to induce syngraft immunity. These results provide strong evidence that amino acid sequence encoded by the second exon of the Ad5 E1A message is required, either directly or indirectly, for the induction of both Ad-specific CTL and Ad TSTA.

Adenovirus Early Proteins↗
PubMed1989

Induction of transcription factor AP-1 by adenovirus E1A protein and cAMP.

Treatment of adenovirus-infected mouse S49 cells with cAMP analogs leads to the transcriptional induction of early viral genes. E1A proteins and cAMP work in synergy to activate several of these genes. We now demonstrate that the transcription factor AP-1 is modestly induced by cAMP in S49 cells and induced to significantly higher levels by cAMP in the presence of E1A proteins. Cytoplasmic levels of c-fos and junB mRNAs are rapidly increased by cAMP, and the induction is substantially stronger in the presence of E1A protein. The AP-1 activity binds efficiently to both AP-1 and activating transcription factor (ATF)/cAMP response element binding protein (CREB)-binding sites present in E1A-inducible promoters and presumably plays a role in the transcriptional activation of adenovirus genes by E1A proteins and cAMP.

Adenovirus Early Proteins↗
PubMed1989

An adenovirus early region 4 gene product is required for induction of the infection-specific form of cellular E2F activity.

E2F is a cellular, sequence-specific DNA-binding factor that binds to pairs of sites that occur upstream of the E1A and E2 early mRNA cap sites. During adenovirus infection, there is induction of a form of E2F that binds cooperatively to the pair of sites in the E2 control region. Production of the infection-specific E2F activity is dependent on early region 4 (E4), as extracts of cells infected with a mutant that lacks E4 did not contain this activity. Instead, two new forms of E2F were seen with the E4 mutant. Infection with mutant viruses unable to make E1A gene products produced the wild-type infection-specific E2F activity after a delay. Mutations in the E1B-55 kD-, E1B-21 kD-, E2-72 kD-, and E3-coding regions had no effect on production of infection-specific E2F. Analysis of cell lines confirmed the results obtained with mutant viruses. Cells that expressed E1A but not E4 genes (e.g., 293 cells) did not contain infection-specific E2F. Cell lines that expressed the E4 gene contained the activity. These observations demonstrate that E4 participates in the infection-induced change in E2F-binding activity. The data are consistent with E1A playing an indirect role in the process by mediating the efficient expression of E4 gene products which, in turn, induce the alteration in E2F activity.

Adenoviridae Infections↗
PubMed1989

Adeno-associated virus P5 promoter contains an adenovirus E1A-inducible element and a binding site for the major late transcription factor.

Activity of the adeno-associated virus P5 transcriptional control region was found to be induced by adenovirus E1A gene products. A pair of adjacent sequence elements was found to mediate both basal and E1A-induced P5 activity. The first element is a binding site for the major late transcription factor (MLTF), a factor first identified on the basis of its binding to a specific sequence within the adenovirus major late promoter. The second element is a tandemly repeated 10-base-pair sequence whose relationship to previously described binding sites is unclear. Each element individually conferred E1A responsiveness on a heterologous promoter, and deletion analysis demonstrated that each contributed to the level of P5 activity in the presence of E1A products both in transfection- and infection-based assays. Although deletion of the MLTF binding site led to reduced P5 transcriptional activity in the presence of E1A proteins, the deletion generated enhanced P5 basal activity in the absence of the transcriptional activator. The negative effect of the MLTF binding site in the absence of activator and its positive effect in the presence of activator combine to enhance the magnitude of the response by the P5 control region to E1A gene products.

Adenovirus Early Proteins↗