Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

Deletion analysis and alternative splicing define a transactivation inhibitory domain in human oncoprotein REL

Misregulation of REL, a nuclear factor-kappaB family transcription factor, has been implicated in several human lymphoid malignancies. REL has a conserved N-terminal DNA-binding/dimerization domain called the Rel homology domain (RHD) and a C-terminal transactivation domain (TAD). Here, we define the sequences (amino acids (aa) 323-422) between the RHD and TAD as a REL inhibitory domain (RID) because deletion of these sequences increases both REL transactivation and DNA binding. Furthermore, we have characterized two REL mRNA splice variants that encode proteins with alterations near RID: one lacking exon 9 sequences (aa 308-330; RELDelta9) and one with an exonized Alu fragment insertion of 32 aa after aa 307 (REL+Alu). Deletion of RID or exon 9-encoded sequences increases transactivation by GAL4-REL by approximately threefold. Moreover, deletion of RID or exon 9 sequences increases transactivation by full-length REL from certain kappaB site-containing promoters and increases DNA binding by REL. Deletion of RID does not affect REL's ability to transform chicken spleen cells. Reverse transcriptase-polymerase chain reaction analysis of mRNA from both primary lymphoma samples and several transformed tissue culture cell lines indicates that the RELDelta9 splice variant is preferentially expressed in lymphoma, suggesting that the REL transcript lacking exon 9 could serve as a marker for certain types of lymphoid tumors.

Introduction to NF-kappaB: players, pathways, perspectives

This article serves as an introduction to the collection of reviews on nuclear factor-kappaB (NF-kappaB). It provides an overview of the discovery and current status of NF-kappaB as a research topic. Described are the structures, activities and regulation of the proteins in the NF-kappaB family of transcription factors. NF-kappaB signaling is primarily regulated by inhibitor kappaB (IkappaB) proteins and the IkappaB kinase complex through two major pathways: the canonical and non-canonical NF-kappaB pathways. The organization and focus of articles included in the following reviews are described, as well as likely future areas of research interest on NF-kappaB.

Mutations in the NF-kappaB signaling pathway: implications for human disease

The nuclear factor-kappa B (NF-kappaB) signaling pathway is a multi-component pathway that regulates the expression of hundreds of genes that are involved in diverse and key cellular and organismal processes, including cell proliferation, cell survival, the cellular stress response, innate immunity and inflammation. Not surprisingly, mis-regulation of the NF-kappaB pathway, either by mutation or epigenetic mechanisms, is involved in many human and animal diseases, especially ones associated with chronic inflammation, immunodeficiency or cancer. This review describes human diseases in which mutations in the components of the core NF-kappaB signaling pathway have been implicated and discusses the molecular mechanisms by which these alterations in NF-kappaB signaling are likely to contribute to the disease pathology. These mutations can be germline or somatic and include gene amplification (e.g., REL), point mutations and deletions (REL, NFKB2, IKBA, CYLD, NEMO) and chromosomal translocations (BCL-3). In addition, human genetic diseases are briefly described wherein mutations affect protein modifiers or transducers of NF-kappaB signaling or disrupt NF-kappaB-binding sites in promoters/enhancers.

Introduction to NF-kappaB: players, pathways, perspectives

This article serves as an introduction to the collection of reviews on nuclear factor-kappaB (NF-kappaB). It provides an overview of the discovery and current status of NF-kappaB as a research topic. Described are the structures, activities and regulation of the proteins in the NF-kappaB family of transcription factors. NF-kappaB signaling is primarily regulated by inhibitor kappaB (IkappaB) proteins and the IkappaB kinase complex through two major pathways: the canonical and non-canonical NF-kappaB pathways. The organization and focus of articles included in the following reviews are described, as well as likely future areas of research interest on NF-kappaB.

Mutation of an IKK phosphorylation site within the transactivation domain of REL in two patients with B-cell lymphoma enhances REL's in vitro transforming activity

The human c-rel proto-oncogene (REL) encodes a subunit of the nuclear factor-kappaB (NF-kappaB) transcription factor. In this report, we have identified an identical point mutation in two human B-cell lymphomas (follicular (FL) and mediastinal) that changes serine (Ser)525 (TCA) to proline (Pro) (CCA) within the REL transactivation domain. This mutation was not identified in a similarly sized cohort of healthy individuals. In the mediastinal B-cell lymphoma, the mutation in REL is of germ-line origin. In both tumors, the S525P mutant allele is over-represented. REL-S525P shows enhanced in vitro transforming activity in chicken spleen cells. REL-S525P has a reduced ability to activate the human manganese superoxide dismutase (MnSOD) promoter in A293 cells; however, the MnSOD protein shows increased expression in REL-S525P-transformed chicken spleen cells as compared to wild-type REL-transformed cells. Ser525 is a site for phosphorylation by IkappaB kinase (IKK) in vitro. The S525P mutation reduces IKKalpha- and tumor necrosis factor (TNF)alpha-stimulated transactivation by a GAL4-REL protein. Furthermore, REL-S525P-transformed chicken spleen cells are more resistant to TNFalpha-induced cell death than cells transformed by wild-type REL. These results suggest that the S525P mutation contributes to the development of human B-cell lymphomas by affecting an IKKalpha-regulated transactivation activity of REL.

Good cop, bad cop: the different faces of NF-kappaB

Complexes formed from the nuclear factor kappaB (NF-kappaB) family of transcription factors are ubiquitously expressed and are induced by a diverse array of stimuli. This results in their becoming activated in a wide variety of different settings. While the functions of NF-kappaB in many of these contexts have been the subject of intense research and are now well established, it is also clear that there is great diversity in the effects and consequences of NF-kappaB activation. NF-kappaB subunits do not necessarily regulate the same genes, in an identical manner, in all of the different circumstances in which they are induced. This review will discuss the different functions of NF-kappaB, the pathways that modulate NF-kappaB subunit activity and, in contrast to its more commonly thought of role as a promoter of cancer cell growth and survival, the ability of NF-kappaB, under some circumstances, to behave as a tumor suppressor.

Malignant transformation of primary chicken spleen cells by human transcription factor c-Rel

Rel/NF-kappaB transcription factors control a variety of cellular processes, such as cell growth and apoptosis, that are relevant to oncogenesis, and mutations in genes encoding Rel/NF-kappaB transcription factors have been found in several human lymphoid cell cancers. In this study, we have used a sensitive cell outgrowth assay to demonstrate that wild-type human c-Rel can malignantly transform primary chicken spleen cells, and that transformation by c-Rel is accelerated by co-expression of Bc1-2. Full-length mouse c-Rel can also transform chicken spleen cells. These results are the first demonstration of a lymphoid cell malignant transforming ability for mammalian Rel/NF-kappaB transcription factors, and implicate c-Rel as a molecular target for cancer therapeutics.

The chicken RelB transcription factor has transactivation sequences and a tissue-specific expression pattern that are distinct from mammalian RelB

Rel/NF-kappaB proteins are eukaryotic transcription factors that control the expression of genes involved in a large variety of cellular processes. Rel proteins share a highly conserved DNA-binding/dimerization domain called the Rel Homology (RH) domain. We have constructed and characterized a composite cDNA encoding most of the chicken RelB transcription factor. The predicted chicken RelB protein has a high degree of sequence similarity to other vertebrate RelB proteins within the RH domain, but is much less conserved outside this domain. Chicken RelB does not bind DNA as a homodimer, but forms DNA-binding heterodimers with NF-kappaB p50 or p52. Overexpressed chicken RelB localizes to the nucleus in chicken embryo fibroblasts, and the nonconserved C-terminal sequences of chicken RelB contain a transactivation domain that functions in chicken and mouse fibroblasts. Thus, chicken RelB has functional properties similar to other vertebrate RelB proteins. However, Western blotting of diverse chicken tissues indicates that chicken RelB is more widely expressed than mammalian RelB.

LIM domain protein Trip6 has a conserved nuclear export signal, nuclear targeting sequences, and multiple transactivation domains

Trip6 is a member of a subfamily of LIM domain proteins, including also zyxin, LPP, Ajuba, and Hic-5, which localize primarily to focal adhesion plaques. However, in this report, we demonstrate that Trip6 is largely in the nucleus in cells treated with leptomycin B, suggesting that Trip6 shuttles between nuclear and cytoplasmic compartments and that nuclear export of Trip6 is dependent on Crm1. Consistent with this finding, we have identified a nuclear export signal (NES) in Trip6, and mutation of this NES also results in sequestration of Trip6 in the nucleus. Addition of the Trip6 NES to the nuclear v-Rel oncoprotein redirects v-Rel to the cytoplasm. Trip6 also has at least two sequences that can direct cytoplasmic beta-galactosidase to the nucleus. Using GAL4 fusion proteins and reporter gene assays, we demonstrate that Trip6 has multiple transactivation domains, including one that appears to overlap with sequences of the NES. In vitro- or in vivo-synthesized Trip6, however, does not bind to DNA-cellulose. Taken together, these results are consistent with Trip6, and other members of this LIM protein family, having a role in relaying signals between focal adhesion plaques and the nucleus.

Three mutations in v-Rel render it resistant to cleavage by cell-death protease caspase-3

The retroviral oncoprotein v-Rel is a transcriptional activator in the Rel/NF-kappa B family. v-Rel causes rapidly fatal lymphomas in young chickens, and transforms and immortalizes chicken lymphoid cells in vitro. Several mutations that have enhanced the oncogenicity of v-Rel have been selected during in vitro and in vivo passage of v-Rel-containing retroviruses. In this report, we show that the C-terminal deletion and two point mutations (Asp-->Gly at residue 91 and Asp-->Asn at residue 437) in v-Rel make it resistant to cleavage by the cell-death protease caspase-3. In contrast, c-Rel, which has Asp residues at these sites, can be cleaved by caspase-3 in vitro as well as in vivo in cells induced to undergo apoptosis. We have characterized activities of v-Rel mutants with recreated single caspase-3 cleavage sites, two cleavage sites, or an introduced artificial cleavage site. All of these mutant v-Rel proteins are sensitive to caspase-3 cleavage in vitro, and show wild-type activity in terms of nuclear localization in chicken fibroblasts and DNA binding in vitro. Moreover, all caspase-3-sensitive v-Rel mutants transform chicken spleen cells in vitro and induce fatal lymphoid tumors in vivo to approximately the same extent as wild-type v-Rel. As with v-Rel mutants, caspase-3-resistant c-Rel mutants behave similarly to caspase-3-sensitive wild-type c-Rel in terms of DNA binding, transcriptional activation, in vitro transformation, and tumorigenicity. Mammalian c-Rel proteins can also be cleaved by caspase-3 in vitro, and a c-Rel mutant from a human pre-T lymphoma cell line is less sensitive than wild-type human c-Rel to cleavage by caspase-3. Taken together, these results demonstrate that specific mutations render oncogenic forms of Rel proteins resistant to cleavage by a cell-death caspase; however, the biological relevance of this resistance remains unclear. Nevertheless, to our knowledge, this is the first demonstration of mutations in caspase-3 recognition sites occurring during the evolution of an oncogenic protein.

Envelope-dependent transactivation by the retroviral oncoprotein v-Rel is required for efficient malignant transformation of chicken spleen cells

The retroviral oncoprotein v-Rel is a chimeric protein that has 11 helper virus-derived Envelope (Env) amino acids (aa) at its N terminus. Within these N-terminal Env aa of v-Rel there are three aa substitutions compared to the Rev-A helper virus Env. These aa substitutions have previously been shown to impart a number of unique properties onto v-Rel, including increased transforming and transactivating ability. In this study, we have analysed the sequence requirements for the Env aa to influence several properties of v-Rel. Phe residues at aa 3 and 9 are critical for an N-terminal transactivation function of v-Rel, and the analysis of several Env mutants demonstrates that transactivation ability parallels the transforming ability of v-Rel. Substitutions of conservative aa, such as leucine and tyrosine, for Phe 3 and 9 are tolerated for transactivation in chicken embryo fibroblasts and for transformation of chicken spleen cells. In contrast, the substitution of 10 Phe residues at the N terminus of v-Rel does not enable transactivation, indicating that a distinct structure surrounding Phe-3 and Phe-9 is essential for v-Rel function. We also show that the addition of the v-Rel Env aa to the N terminus of human c-Rel can enable it to activate transcription. Taken together, these results indicate that Phe residues at positions 3 and 9 have been selected for their ability to enhance the oncogenicity of v-Rel by increasing its ability to activate transcription.

Mutant envelope residues confer a transactivation function onto N-terminal sequences of the v-Rel oncoprotein

The retroviral oncoprotein v-Rel is a member of the Rel/ NF-kappaB family of transcription factors. v-Rel has multiple changes as compared to the proto-oncoprotein c-Rel, and these changes render v-Rel highly oncogenic in avian lymphoid cells. Previous results have shown that three mutant residues in the eleven helper virus-derived Envelope (Env) amino acids (aa) at the N-terminus of v-Rel are required for its full oncogenicity. In this report, we show that these mutant Env aa also enable sequences in the N-terminal half of v-Rel to activate transcription in yeast and chicken cells, under conditions where the analogous sequences from c-Rel either do not or only weakly activate transcription. Removal of the Env aa from v-Rel or site-directed mutations that revert the three mutant residues to the residues present in the Rev-A helper virus Env protein abolish this transactivation ability of v-Rel. Addition of mutant Env aa onto c-Rel is not sufficient to fully restore the transactivation function; other sequences in the N-terminal half of v-Rel are needed for full transactivating ability. A C terminally-truncated form of NF-kappaB p100 (p85), produced in HUT-78 human leukemic cells, also activates transcription in yeast, under conditions where the normal p52 and p100 proteins do not. Furthermore, transcriptional activation by p85 in yeast is likely to occur through N-terminal sequences. Taken together, these results are consistent with a model in which transactivation by N-terminal Rel Homology (RH) domain sequences in oncogenic Rel family proteins is influenced by sequences outside the RH domain.

Diverse agents act at multiple levels to inhibit the Rel/NF-kappaB signal transduction pathway

Rel/NF-kappaB transcription factors regulate several important physiological processes, including developmental processes, inflammation and immune responses, cell growth, cancer, apoptosis, and the expression of certain viral genes. Therefore, they have also been sought-after molecular targets for pharmacological intervention. As details of the Rel/NF-kappaB signal transduction pathway are revealed, it is clear that modulators of this pathway can act at several levels. Inhibitors of the Rel/NF-kappaB pathway include a variety of natural and designed molecules, including anti-oxidants, proteasome inhibitors, peptides, small molecules, and dominant-negative or constitutively active polypeptides in the pathway. Several of these molecules act as general inhibitors of Rel/NF-kappaB induction, whereas others inhibit specific pathways of induction. Inhibitors of Rel/NF-kappaB are likely to gain stature as treatments for certain cancers and neurodegenerative and inflammatory diseases.

Multiple mutations contribute to the oncogenicity of the retroviral oncoprotein v-Rel

The avian Rev-T retrovirus encodes the v-Rel oncoprotein, which is a member of the Rel/NF-kappaB transcription factor family. v-Rel induces a rapidly fatal lymphoma/leukemia in young birds, and v-Rel can transform and immortalize a variety of avian cell types in vitro. Although Rel/NF-kappaB transcription factors have been associated with oncogenesis in mammals, v-Rel is the only member of this family that is frankly oncogenic in animal model systems. The potent oncogenicity of v-Rel is the consequence of a number of mutations that have altered its activity and regulation: for example, certain mutations decrease its ability to be regulated by IkappaBalpha, change its DNA-binding site specificity, and endow it with new transactivation properties. The study of v-Rel will continue to increase our knowledge of how cellular Rel proteins contribute to oncogenesis by affecting cell growth, altering cell-cycle regulation, and blocking apoptosis. This review will discuss biological and molecular activities of v-Rel, with particular attention to how these activities relate to structure - function aspects of the Rel/NF-kappaB transcription factors.

Control of apoptosis by Rel/NF-kappaB transcription factors

Apoptosis is a physiological process critical for organ development, tissue homeostasis, and elimination of defective or potentially dangerous cells in complex organisms. Apoptosis can be initiated by a wide variety of stimuli, which activate a cell suicide program that is constitutively present in most vertebrate cells. In diverse cell types, Rel/NF-kappaB transcription factors have been shown to have a role in regulating the apoptotic program, either as essential for the induction of apoptosis or, perhaps more commonly, as blockers of apoptosis. Whether Rel/NF-kappaB promotes or inhibits apoptosis appears to depend on the specific cell type and the type of inducer. An understanding of the role of Rel/NF-kappaB transcription factors in controlling apoptosis may lead to the development of therapeutics for a wide variety of human diseases, including neurodegenerative and immune diseases, and cancer.

In vitro-translated diphtheria toxin A chain inhibits translation in wheat germ extracts: analysis of biologically active, caspase-3-resistant diphtheria toxin mutants

The diphtheria toxin A chain (DTA) is a potent cytocidal agent that inactivates elongation factor 2. This activity of DTA inhibits protein synthesis and rapidly leads to cell death through apoptosis. In this paper, we have developed a simple in vitro assay for DTA activity in which in vitro-translated DTA is used to inhibit the translation of proteins in wheat germ extracts. Inhibition of translation by DTA is dependent on cofactor NAD+, and the analysis of an attenuated DTA mutant indicates that this in vitro assay accurately reflects the in vivo activity of DTA. We have also identified aspartic acid at residue 8 (Asp-8) of DTA as a site of cleavage by the cell-death protease caspase-3. Cleavage of DTA by caspase-3 inactivates its ability to inhibit translation in wheat germ extracts. Conservative mutations at Asp-8 render DTA resistant to cleavage by caspase-3, but only slightly affect the ability of DTA to inhibit translation in vitro. Moreover, caspase-3-resistant DTA mutants are toxic in cells in tissue culture. The in vitro assay that we describe here will be useful for the rapid analysis of DTA activity and the development of DTA mutants with altered biological properties that may be of therapeutic value. Lastly, these studies serve as a prototype for the creation of caspase-resistant effector molecules.

Characterization of mouse Trip6: a putative intracellular signaling protein

Trip6 is a human LIM domain-containing protein that has been identified in yeast two-hybrid screens as interacting with a variety of proteins. Trip6 has been proposed to transport signals from the cell surface to the nucleus. In this report, we have characterized a mouse cDNA encoding Trip6. Mouse Trip6 is highly similar to human Trip6, especially in the C-terminal LIM domain region, and the in vitro and in vivo mouse Trip6 cDNA directs the synthesis of a polypeptide with a relative mobility of approx. 57kDa on SDS-polyacrylomide gels. Full-length Trip6 localizes to discrete cytoplasmic patches when overexpressed in chicken embryo fibroblasts, consistent with localization to focal adhesion plaques. However, deletion of the N-terminal 115 amino acids allows Trip6 to enter the nucleus of CEF. A GAL4 fusion protein containing the LIM domain region of mouse Trip6 can activate transcription in yeast and chicken fibroblasts. Our results indicate that the functional domains and properties of mouse Trip6 are highly conserved between humans and mice, and are consistent with a model in which Trip6 relays signals from the cell surface to the nucleus.

Epstein-Barr virus-transforming protein latent infection membrane protein 1 activates transcription factor NF-kappaB through a pathway that includes the NF-kappaB-inducing kinase and the IkappaB kinases IKKalpha and IKKbeta

The Epstein-Barr virus oncoprotein latent infection membrane protein 1 (LMP1) is a constitutively aggregated pseudo-tumor necrosis factor receptor (TNFR) that activates transcription factor NF-kappaB through two sites in its C-terminal cytoplasmic domain. One site is similar to activated TNFRII in associating with TNFR-associated factors TRAF1 and TRAF2, and the second site is similar to TNFRI in associating with the TNFRI death domain interacting protein TRADD. TNFRI has been recently shown to activate NF-kappaB through association with TRADD, RIP, and TRAF2; activation of the NF-kappaB-inducing kinase (NIK); activation of the IkappaB alpha kinases (IKKalpha and IKKbeta); and phosphorylation of IkappaB alpha. IkappaB alpha phosphorylation on Ser-32 and Ser-36 is followed by its degradation and NF-kappaB activation. In this report, we show that NF-kappaB activation by LMP1 or by each of its effector sites is mediated by a pathway that includes NIK, IKKalpha, and IKKbeta. Dominant negative mutants of NIK, IKKalpha, or IKKbeta substantially inhibited NF-kappaB activation by LMP1 or by each of its effector sites.

Phosphorylation of IkappaB-alpha inhibits its cleavage by caspase CPP32 in vitro

IkappaB proteins function as direct regulators of Rel/NF-kappaB transcription complexes. We show that the cell-death protease CPP32 (caspase-3) in vitro specifically cleaved chicken and human IkappaB-alpha at a conserved Asp-Ser sequence. This cleavage site appears to be identical to the site at which chicken IkappaB-alpha is cleaved in vivo in temperature-sensitive v-Rel-transformed chicken spleen cells undergoing apoptosis. Other caspases, namely interleukin-1beta-converting enzyme (caspase-1) and Ich-1 (caspase-2), did not cleave IkappaB-alpha. CPP32 also cleaved mammalian IkappaB-beta in vitro at the analogous Asp-Ser sequence. Cleavage of IkappaB-alpha by CPP32 was blocked by serine phosphorylation of IkappaB-alpha. Cleavage of IkappaB-alpha by a CPP32- like protease could generate a constitutive inhibitor of Rel transcription complexes. This report provides evidence for a direct biochemical interaction between the NF-kappaB signaling pathway and a cell-death protease signaling pathway.

Introduction: The Rel/NF-kappaB signal transduction pathway

No abstract Copyright 1997Academic Press Limited

Bcl-2 and CrmA have different effects on transformation, apoptosis and the stability of I kappa B-alpha in chicken spleen cells transformed by temperature-sensitive v-Rel oncoproteins

The retroviral oncoprotein v-Rel is a member of the Rel/ NF-kappa B family of transcription factors. We have previously characterized two v-Rel mutants (v-G37E and v-R273H) that are temperature-sensitive (ts) for transformation and immortalization of chicken spleen cells in vitro. We have now constructed vectors for the co-expression of wild-type or ts mutant v-Rel proteins and the anti-apoptosis proteins Bcl-2 or CrmA. The formation of v-Rel-transformed colonies is enhanced in the presence of overexpressed Bcl-2. Moreover, co-expression of Bcl-2 suppresses apoptosis that is induced when ts v-Rel-transformed cells are shifted to the non-permissive temperature. However, co-expression of Bcl-2 in these cells does not affect ts functions of v-Rel, such as DNA binding and stabilization of I kappa B-alpha. In contrast, co-expression of CrmA does not suppress apoptosis, but does block an amino-terminal proteolysis of I kappa B-alpha that occurs in ts v-G37E-transformed cells shifted to the nonpermissive temperature, indicating that an ICE-like protease activity is not involved in apoptosis in these cells but is involved in proteolysis of I kappa B-alpha. In addition, CrmA can block cycloheximide-induced amino-terminal processing of I kappa B-alpha in spleen cells transformed by wild-type v-Rel. In summary, these results suggest that v-Rel immortalizes chicken spleen cells through a pathway that involves the Bcl-2 family of proteins, and suggest that one pathway of proteolysis of I kappa B-alpha involves an ICE-like protease.

Interaction of the v-Rel oncoprotein with NF-kappaB and IkappaB proteins: heterodimers of a transformation-defective v-Rel mutant and NF-2 are functional in vitro and in vivo

The v-Rel oncoprotein of the avian Rev-T retrovirus is a member of the Rel/NF-kappa B family of transcription factors. The mechanism by which v-Rel malignantly transforms chicken spleen cells is not precisely known. To gain a better understanding of functions needed for transformation by v-Rel, we have now characterized the activities of mutant v-Rel proteins that are defective for specific protein-protein interactions. Mutant v-delta NLS, which has a deletion of the primary v-Rel nuclear localizing sequence, does not interact efficiently with I kappa B-alpha but still transforms chicken spleen cells approximately as well as wild-type v-Rel, indicating that interaction with I kappa B-alpha is not essential for the v-Rel transforming function. A second v-Rel mutant, v-SPW, has been shown to be defective for the formation of homodimers, DNA binding, and transformation. However, we now find that v-SPW can form functional DNA-binding heterodimers in vitro and in vivo with the cellular protein NF-kappa B p-52. Most strikingly, coexpression of v-SPW and p52 from a retroviral vector can induce the malignant transformation of chicken spleen cells, whereas expression of either protein alone cannot. Our results are most consistent with a model wherein Rel homodimers or heterodimers must bind DNA and alter gene expression in order to transform lymphoid cells.

Genetic analysis of growth inhibition by GAL4-L kappa B-alpha in Saccharomyces cerevisiae

I kappa B proteins bind to and regulate Rel/NF- kappa B transcription factors. We showed previously that a fusion protein (GAL4-p40) containing the DNA-binding domain of GAL4 and sequences of chicken l kappa B-alpha (p40) inhibits growth in the yeast Saccharomyces cerevisiae. We now show that p40 must be bound to DNA to inhibit yeast growth, p40 proteins, bound to DNA either as GAL4 or LEXA fusion proteins, inhibit yeast growth. In contrast, p40 proteins that cannot bind to DNA, such as full-length p40, a GAL4-l kappa B fusion protein containing a mutant GAL4 DNA-binding domain, and a fusion protein (GAD-p40) containing the transcriptional activation domain of GAL4 fused to p40, each failed to inhibit cell growth. As with GAL4-VP16, GAL4-p40 needs a functional cellular ADA2 gene to exert its growth-inhibitory effect in S. cerevisiae. Using a high copy suppression strategy, we have isolated three S. cerevisiae genes that restore normal growth to yeast expressing GAL4-p40 or LEXA-p40. We have termed these rescuing genes collectively as SIK genes, for "Suppressors of 1 kappa B." Expression of the SIK genes specifically suppresses the growth-inhibitory activity of GAL4-p40 and LEXA-p40 because SIK gene expression cannot block GAL4-VP16-mediated growth inhibition in S. cerevisiae. SIK1 encodes a novel protein that contains a COOH-terminal repeat that has been found in many microtubule-binding proteins. SIK2 encodes NH2-terminal acetyltransferase, and SIK3 encodes the yeast ribosomal S4 protein. None of the SIK proteins binds directly to p40 sequences in vitro, suggesting that the SIK proteins are likely to act downstream of the direct point of growth inhibition by GAL4-p40. Our results may be useful for devising strategies for identifying vertebrate inhibitors of l kappa B proteins and of other proteins that inhibit growth in S. cerevisiae.

The v-Rel oncoprotein blocks apoptosis and proteolysis of I kappa B-alpha in transformed chicken spleen cells

The v-Rel oncoprotein of the avian Rev-T retrovirus malignantly transforms chicken spleen cells in vivo and in vitro. We previously described two temperature-sensitive (ts) mutants of v-Rel (v-G37E and v-R273H) that show a ts ability to transform chicken spleen cells and to bind to DNA in vitro. We now show that spleen cell lines transformed by ts v-Rel proteins at the permissive temperature undergo apoptosis when cells are shifted to the nonpermissive temperature. The levels of most proteins (including v-Rel, p53, c-Myc, Rb and Bcl-2) do not change in these cells even at advanced stages of apoptosis. However, the chicken I kappa B-alpha protein (also called p40), which is in a complex with v-Rel in transformed cells, is degraded when ts v-Rel-transformed cells are shifted to the nonpermissive temperature. In v-R273H-transformed cells, p40 is degraded without the appearance of proteolytic intermediates. In contrast, in v-G37E-transformed cells, p40 is cleaved to an intermediate species that is missing approximately 3-4 kDa from its amino terminus. This truncated form of p40 is found in a detergent-insoluble fraction and can also be detected in wild-type v-Rel-transformed cells that are induced to undergo apoptosis by treatment with cycloheximide. Both ts v-Rel proteins are ts for interaction with p40 in vitro. The results reported here indicate that v-Rel blocks a normal pathway of programmed cell death and that I kappa B-alpha can undergo multiple degradative pathways, which can be induced by alterations in the structure of the Rel protein to which it is bound.

Interaction of the v-Rel oncoprotein with cellular transcription factor Sp1

We previously showed that v-Rel, the oncoprotein of the avian retrovirus Rev-T, can increase expression from promoters containing binding sites for the cellular transcription factor Sp1 in chicken embryo fibroblasts (S. Sif, A.J. Capobianco, and T.D. Gilmore, Oncogene 8:2501-2509, 1993). In those experiments, v-Rel appeared to increase the transactivating function of Sp1; that is, v-Rel stimulated transactivation by a GAL4-Sp1 protein that lacked the Sp1 DNA-binding domain. We have now shown that in vitro-synthesized v-Rel and GAL4-Sp1 form a complex that can be immunoprecipitated with either anti-Sp1 or anti-v-Rel antiserum. We have also shown that a glutathione S-transferase (GST)-Sp1 fusion protein can specifically interact with in vitro-translated v-Rel and with in vivo-synthesized v-Rel from transformed chicken spleen cells. In addition, we have found that the abilities of wild-type and two mutant forms of v-Rel to increase transactivation by Sp1 in vivo correlate with their abilities to interact with Sp1 in vitro. The sequences important for the interaction of v-Rel with Sp1 in vitro have been mapped to the first 147 amino acids of v-Rel. Other Rel proteins, such as c-Rel, RelA, p52, and p50, were also able to form a complex with Sp1 in vitro. These results suggest that v-Rel increases expression from Sp1 site-containing promoters by functionally interacting with Sp1 and that cellular Rel proteins and Sp1 are likely to interact to influence transcription from natural promoters.

Characterization of a chicken cDNA encoding the retinoblastoma gene product

We have isolated a chicken cDNA that encodes the retinoblastoma susceptibility gene product (RB). The predicted amino acid sequence of the chicken RB protein is highly similar to that of the mouse, human and Xenopus RB proteins in regions of known functions; however, chicken RB has distinct species-specific differences, including a shorter N-terminal region as compared to the mouse and human RB proteins. In vitro-translated chicken RB co-migrates on SDS-polyacrylamide gels with endogenous RB synthesized in transformed chicken spleen cells. Finally, chicken RB is located in the nucleus of chicken embryo fibroblasts when overexpressed from a retroviral vector.

The I kappa B proteins: members of a multifunctional family

The I kappa B proteins bind to Rel/NF-kappa B transcription factors and modulate their activities. Although originally described only as cytoplasmic inhibitors of Rel/NF-kappa B transcription complexes, it is now clear that I kappa B proteins also have other functions.

NF-kappa B p100 is one of the high-molecular-weight proteins complexed with the v-Rel oncoprotein in transformed chicken spleen cells

The Rel/NF-kappa B family of proteins includes several interacting cellular transcription factors and the v-Rel oncoprotein of the avian Rev-T retrovirus. We report the isolation of a chicken cDNA for the NF-kappa B p52 precursor protein p100. Full-length p100 only weakly binds DNA in vitro; removal of the ankyrin-like repeats generates C-terminally truncated p100 proteins (like p52) that have an increased ability to bind an oligonucleotide containing a kappa B site. In addition, we show that chicken p100 is identical to a protein previously designated p115, which is found in a complex with v-Rel in transformed chicken spleen cells. Furthermore, p100 and v-Rel can form a complex when synthesized in vitro. Using cDNAs for chicken NF-kappa B p105, NF-kappa B p100, c-Rel, and v-Rel, we show that one of the complexes in v-Rel-transformed spleen cells can be reconstituted in vitro.

Temperature-sensitive transforming mutants of the v-rel oncogene

By making site-directed mutations in the avian retroviral oncogene v-rel, we created two temperature-sensitive (ts) transforming mutants; these changes were analogous to mutations previously shown to confer a ts function onto the Dorsal protein of Drosophila melanogaster. Chicken spleen cells infected with the ts v-rel mutants formed colonies in agar at 36.5 degrees C but not at 41.5 degrees C. In addition, spleen cells derived from the ts v-rel-transformed colonies could be propagated in liquid culture at 36.5 degrees C but rapidly senesced at 41.5 degrees C. Both mutant v-Rel proteins were also ts for DNA binding in vitro. These mutants may be valuable for identifying genes directly regulated by v-rel.

The v-Rel oncoprotein increases expression from Sp1 site-containing promoters in chicken embryo fibroblasts

The v-Rel oncoprotein of the avian Rev-T retrovirus is a member of a family of related transcription factors, which also includes the subunits of NF-kappa B and several other interacting cellular proteins. We show here that v-Rel specifically increased expression from a reporter plasmid containing multiple Sp1 binding sites approximately sixfold in chicken embryo fibroblasts (CEFs), even though v-Rel did not bind directly to these sites. v-Rel also increased expression from a reporter plasmid containing a human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) in which the kappa B binding sites were mutated but which still contained intact Sp1 binding sites. The increase in Sp1-site transactivation does not precisely correlate with transformation by v-Rel since one non-transforming v-Rel mutant still induced expression from the Sp1 site-containing promoter. v-Rel appears to increase expression from Sp1 site-containing promoters by affecting the transactivation domain of Sp1, since v-Rel increased the activity of a Gal4-Sp1 fusion protein, which contains the Sp1 transactivation domain but lacks the Sp1 DNA-binding domain. As compared with v-Rel, c-Rel induced only a slight increase in expression from the reporter plasmid containing Sp1 sites. However, v-Ras and v-Src (but not v-Myb) induced increases in transcription from the reporter plasmid containing Sp1 sites to the same extent as v-Rel, but through pathways that appear to be independent from v-Rel. These results suggest that certain oncoproteins might increase transcription from many genes that contain Sp1 binding sites, and that this might be important for certain aspects of transformation by these proteins.

Transformation by the vRel oncoprotein requires sequences carboxy-terminal to the Rel homology domain

The vRel oncoprotein of the avian Rev-T retrovirus is a member of the Rel/NF-kappa B family of transcription factors. The highly conserved amino-terminal Rel Homology (RH) domain in these proteins is required for DNA binding, protein-protein interactions and nuclear localization, and many mutations within this domain abolish transformation by vRel. We demonstrate here that overexpression of the vRel RH domain alone is insufficient to induce transformation of chicken spleen cells, indicating that sequences from the nonconserved carboxy terminus are necessary for the vRel transforming function. Therefore, we constructed and assayed several vRel mutants with deletions of carboxy-terminal sequences. These mutant vRel proteins did not transform spleen cells with equal efficiency, even though they were functionally similar by several other criteria. Our results demonstrate that there are two regions (aa 389 to 432 and aa 437 to 503) within the carboxy-terminal half of vRel that are important for transformation: mutant vRel proteins containing the RH domain and one or both of these carboxy-terminal regions can transform at roughly wild-type levels. Analysis of Gal4 fusion proteins containing carboxy-terminal sequences from the vRel mutants indicated that there is a correlation between the ability of these mutant proteins to transform avian spleen cells and their ability to activate transcription. These observations suggest that vRel induces malignant transformation by directly altering gene expression.

GAL4-I kappa B alpha and GAL4-I kappa B gamma activate transcription by different mechanisms

I kappa B proteins regulate Rel/NF-kappa B transcription complexes through a direct protein-protein interaction. In addition, we have previously shown that certain I kappa B proteins (I kappa B alpha and I kappa B gamma) can act as activators of transcription when fused to the DNA-binding domain of GAL4. We now show that a mutant chicken I kappa B alpha protein that cannot interact with Rel proteins in vitro did not activate transcription when fused to GAL4 in chicken embryo fibroblasts (CEF) and Saccharomyces cerevisiae, and did not inhibit growth in yeast; in contrast, an I kappa B alpha mutant that can still interact in vitro with Rel proteins activated transcription in both CEF and yeast and inhibited growth in yeast. In CEF, GAL4-I kappa B alpha mediated transcription activation was inhibited by co-transfection with an expression vector for a RelA (p65) protein that contained sequences needed for interaction with I kappa B alpha but that was deleted of its transcription activation domain. Therefore, it appears that GAL4-I kappa B alpha activates transcription by interacting with an endogenous Rel family protein in CEF. In contrast, the activation domain from I kappa B gamma behaved as a genuine acidic activator of transcription and did not inhibit growth when expressed in yeast. Since transcription activation and growth inhibition by GAL4-I kappa B alpha mutants in yeast correlated with their ability to interact with vertebrate Rel proteins, our results suggest that these activities of GAL4-I kappa B alpha are mediated through interaction with a Rel-like protein in yeast, which is important for cell growth.

v-Rel and c-Rel are differentially affected by mutations at a consensus protein kinase recognition sequence

The avian retroviral oncoprotein v-Rel and its cellular homolog c-Rel are members of a family of related site-specific DNA-binding proteins. Towards the carboxy-terminal end of the highly conserved Rel homology (RH) domain in the majority of Rel proteins, there is a consensus recognition sequence for protein kinase A (PK-A). We have investigated the importance of this sequence (Arg-Arg-Pro-Ser) for several functional properties of v-Rel and c-Rel. Disruption of the PK-A sequence by a two amino acid insertion between the arginine and the proline residues completely abolished the ability of v-Rel and c-Rel to bind a kappa B site in vitro. When the phosphorylatable serine in this sequence (Ser-275 in v-Rel, Ser-266 in c-Rel) was replaced by an alanine, DNA binding by v-Rel was not affected, whereas the ability of c-Rel to bind DNA was reduced approximately fourfold by this mutation. Similarly, a serine to tryptophan change greatly reduced the DNA-binding ability of c-Rel, whereas v-Rel was not appreciably affected by this change. When this serine was replaced by an acidic amino acid, DNA binding by v-Rel was reduced approximately twofold and the DNA-binding activity of c-Rel was nearly abolished. Glutaraldehyde cross-linking experiments indicated that mutations at the PK-A recognition site that reduced DNA binding also negatively affected protein oligomerization, which is likely to be responsible for the reduced ability of mutant v-Rel and c-Rel proteins to bind DNA. Domain-swapping experiments showed that structural differences between v-Rel and c-Rel in the central region of the proteins are primarily responsible for the higher sensitivity of c-Rel to a serine to alanine mutation in the PK-A site. One difference between v-Rel and c-Rel, a glutamine to alanine change in v-Rel located three amino acids carboxy-terminal to the PK-A phosphorylatable serine (Ala-278 in v-Rel; Glu-269 in c-Rel), is mainly responsible for the lack of an effect on DNA binding by v-Rel when Ser-275 is replaced by alanine. That is, a v-Rel double mutant (v-275A/278E) showed reduced DNA-binding and transforming abilities as compared with v-Rel and v-275A. Similarly, the mutations in c-Rel that affected DNA binding showed a corresponding effect on the ability of c-Rel proteins to activate transcription in yeast from a reporter gene containing upstream Rel binding sites.(ABSTRACT TRUNCATED AT 400 WORDS)