Structure of the NF-kappa B p50 homodimer bound to DNA

Constitutive NF-kappa B activation, enhanced granulopoiesis, and neonatal lethality in I kappa B alpha-deficient mice

Transcription factors belonging to the NF-kappa B family are controlled by inhibitory I kappa B proteins, mainly I kappa B alpha and I kappa B beta. Apparently normal at birth, I kappa B alpha-/- mice exhibit severe runting, skin defects, and extensive granulopoiesis postnatally, typically dying by 8 days. Hematopoietic tissues from these mice display elevated levels of both nuclear NF-kappa B and mRNAs of some, but not all, genes thought to be regulated by NF-kappa B. NF-kappa B elevation results in these phenotypic abnormalities because mice lacking both I kappa B alpha and the p50 subunit of NF-kappa B show a dramatically delayed onset of abnormalities. In contrast to hematopoietic cells, I kappa B alpha-/- embryonic fibroblasts show minimal constitutive NF-kappa B, as well as normal signal-dependent NF-kappa B activation that is concomitant with I kappa B beta degradation. Our results indicate that I kappa b beta, but not I kappa B alpha, is required for the signal-dependent activation of NF-kappa B in fibroblasts. However, I kappa B alpha is required for the postinduction repression of NF-kappa B in fibroblasts. These results define distinct roles for the two forms of I kappa B and demonstrate the necessity for stringent control of NF-kappa B.

Interactions of a Rel protein with its inhibitor

Cactus, a Drosophila homologue of I kappa B, binds to and inhibits Dorsal, a homologue of the p50 and p65 components of NF-kappa B. We describe experiments in yeast with various Dorsal and Cactus derivatives showing that Cactus blocks the DNA binding and nuclear localization functions of Dorsal. In contrast, Dorsal's transcriptional activating region is functional in the Dorsal-Cactus complex. We identify two Dorsal mutants, Dorsal C233R and Dorsal S234P, that escape Cactus inhibition in vivo, and we show that these mutants fail to interact with Cactus in vitro. From this and data of others, we identify the likely surface of Dorsal that binds Cactus. We also describe a modified PCR mutagenesis procedure, easier to use than conventional methods, that produces a library of high complexity.

Co-crystallization of an ETS domain (PU.1) in complex with DNA. Engineering the length of both protein and oligonucleotide

The PU.1 transcription factor is a member of the ets gene family of regulatory proteins. These molecules play a role in normal development and also have been implicated in malignant processes such as the development of erythroid leukemia. The Ets proteins share a conserved DNA-binding domain (the ETS domain) that recognizes a purine-rich sequence with the core sequence: 5'-C/AGGAA/T-3'. This domain binds to DNA as a monomer, unlike many other DNA-binding proteins. The ETS domain of the PU.1 transcription factor has been crystallized in complex with a 16-base pair oligonucleotide that contains the recognition sequence. The crystals formed in the space group C2 with a = 89.1, b = 101.9, c = 55.6 A, and beta = 111.2 degrees and diffract to at least 2.3 A. There are two complexes in the asymmetric unit. Production of large usable crystals was dependent on the length of both protein and DNA components, the use of oligonucleotides with unpaired A and T bases at the termini, and the presence of polyethylene glycol and zinc acetate in the crystallization solutions. This is the first ETS domain to be crystallized, and the strategy used to crystallize this complex may be useful for other members of the ets family.

Conformational changes induced by DNA binding of NF-kappa B

The transcription factor NF-kappa B makes extensive contacts with its recognition site over one complete turn of the double helix. Structural transitions, in both protein and DNA, that accompany formation of the DNA-protein complex were analysed by proteinase sensitivity and circular dichroism (CD) spectroscopy. In the absence of DNA chymotrypsin cleaved p50 after residues Y60 and N78, while proteinase K cleaved p50 after residues S74 and Q180. Previous experiments had indicated that trypsin cleaved p50 after K77. Cleavages after Y60, S74, K77 and N78 were blocked in the presence of bound DNA, whereas cleavage after Q180 was enhanced. Y60, S74, K77 and N78 are all located in the p50 N-terminal domain AB loop, whereas Q180 is located in the mainly alpha-helical region between p50 N-terminal domain beta-strands G' and H. As only Y60 makes direct contact with the DNA it is likely that the AB loop is highly unstructured in the absence of DNA, but is held in a rigid, proteinase-resistant structure by bound DNA. These conclusions were supported by CD spectroscopic studies of recombinant p50 and p65 homodimers, which indicated that both species changed conformation when binding DNA. Examination of the near UV CD spectra revealed that with some DNA sequences the bound and free forms of the DNA assumed different conformations. While this was evident for a fully symmetrical, high affinity recognition site DNA, it was not apparent with less tightly bound DNA.

Regulation of human immunodeficiency virus type 1 and cytokine gene expression in myeloid cells by NF-kappa B/Rel transcription factors

CD4+ macrophages in tissues such as lung, skin, and lymph nodes, promyelocytic cells in bone marrow, and peripheral blood monocytes serve as important targets and reservoirs for human immunodeficiency virus type 1 (HIV-1) replication. HIV-1-infected myeloid cells are often diminished in their ability to participate in chemotaxis, phagocytosis, and intracellular killing. HIV-1 infection of myeloid cells can lead to the expression of surface receptors associated with cellular activation and/or differentiation that increase the responsiveness of these cells to cytokines secreted by neighboring cells as well as to bacteria or other pathogens. Enhancement of HIV-1 replication is related in part to increased DNA-binding activity of cellular transcription factors such as NF-kappa B. NF-kappa B binds to the HIV-1 enhancer region of the long terminal repeat and contributes to the inducibility of HIV-1 gene expression in response to multiple activating agents. Phosphorylation and degradation of the cytoplasmic inhibitor I kappa B alpha are crucial regulatory events in the activation of NF-kappa B DNA-binding activity. Both N- and C-terminal residues of I kappa B alpha are required for inducer-mediated degradation. Chronic HIV-1 infection of myeloid cells leads to constitutive NF-kappa B DNA-binding activity and provides an intranuclear environment capable of perpetuating HIV-1 replication. Increased intracellular stores of latent NF-kappa B may also result in rapid inducibility of NF-kappa B-dependent cytokine gene expression. In response to secondary pathogenic infections or antigenic challenge, cytokine gene expression is rapidly induced, enhanced, and sustained over prolonged periods in HIV-1-infected myeloid cells compared with uninfected cells. Elevated levels of several inflammatory cytokines have been detected in the sera of HIV-1-infected individuals. Secretion of myeloid cell-derived cytokines may both increase virus production and contribute to AIDS-associated disorders.

Regulation of the DNA binding activity of NF-kappa B

The DNA binding activity of the dimeric sequence-specific transcription factor NF-kappa B can be controlled by a variety of post-translational mechanisms, including interactions with inhibitor proteins and by its redox state. The NF-kappa B family of transcription factors bind to kappa B motif sequences found in promoter and enhancer regions of a wide range of cellular and viral genes. Normally NF-kappa B family proteins are held in the cytoplasm in an inactive, non-DNA binding form by labile I kappa B inhibitor proteins. When the cell is activated by one of a wide range of stimuli, typically those associated with the cellular response to pathogens or stress, proteolytic degradation of I kappa B inhibitor proteins allows active NF-kappa B to translocate to the nucleus where it activates transcription of responsive genes. The initial trigger for I kappa B degradation is a signal-induced site-specific phosphorylation by an as yet unidentified kinase, which appears to target I kappa B for the covalent addition of multiple copies of the ubiquitin polypeptide. This modification subsequently allows the proteolytic degradation of the ubiquitinated I kappa B by the cellular 26S multicatalytic proteinase (proteasome) complex. It was recently shown that increased I kappa B-alpha expression in the cytoplasm leads to I kappa B-alpha accumulating in the nuclear compartment, removing template-bound NF-kappa B, and reducing NF-kappa B-dependent transcription. These NF-kappa B-I kappa B-alpha complexes could then be actively re-exported to the cytoplasm, allowing the cell to respond to further stimuli.

Crystal structure of a conserved protease that binds DNA: the bleomycin hydrolase, Gal6

Bleomycin hydrolase is a cysteine protease that hydrolyzes the anticancer drug bleomycin. The homolog in yeast, Gal6, has recently been identified and found to bind DNA and to act as a repressor in the Gal4 regulatory system. The crystal structure of Gal6 at 2.2 A resolution reveals a hexameric structure with a prominent central channel. The papain-like active sites are situated within the central channel, in a manner resembling the organization of active sites in the proteasome. The Gal6 channel is lined with 60 lysine residues from the six subunits, suggesting a role in DNA binding. The carboxyl-terminal arm of Gal6 extends into the active site cleft and may serve a regulatory function. Rather than each residing in distinct, separable domains, the protease and DNA-binding activities appear structurally intertwined in the hexamer, implying a coupling of these two activities.

The structure of the NF-kappa B p50:DNA-complex: a starting point for analyzing the Rel family

The Rel family comprises a group of structurally related, eukaryotic transcription factors. The similarity extends over about 300 amino acid residues, the Rel homology region, which is responsible for DNA binding and dimerization. Two independently determined structures of homodimeric NF-kappa B p50 bound to DNA show the Rel homology regions and the DNA target sites. The protein consists of two beta-barrel domains connected by a short linker. Five loops per monomer contact the DNA. Different half-site spacings in the two structures lead to different relative orientations of N- and C-terminal domains.

Considerations on the folding topology and evolutionary origin of cadherin domains

Cell-cell adhesion in zonula adherens and desmosomal junctions is mediated by cadherins, and recent crystal structures of the first domain from murine N-cadherin provide a plausible molecular basis for this adhesive action. A structure-based sequence analysis of this adhesive domain indicates that its fold is common to all extracellular cadherin domains. The cadherin folding topology is also shown to be similar to immunoglobulin-like domains and to other Greek-key beta-sandwich structures, as diverse as domains from plant cytochromes, bacterial cellulases, and eukaryotic transcription factors. Sequence similarities between cadherins and these other molecules are very low, however, and intron patterns are also different. On balance, independent origins for a favorable folding topology seem more likely than evolutionary divergence from an ancestor common to cadherins and immunoglobulins.

Signal-induced site-specific phosphorylation targets I kappa B alpha to the ubiquitin-proteasome pathway

The transcription factor NF-kappa B is sequestered in the cytoplasm by the inhibitor protein I kappa B alpha. Extracellular inducers of NF-kappa B activate signal transduction pathways that result in the phosphorylation and subsequent degradation of I kappa B alpha. At present, the link between phosphorylation of I kappa B alpha and its degradation is not understood. In this report we provide evidence that phosphorylation of serine residues 32 and 36 of I kappa B alpha targets the protein to the ubiquitin-proteasome pathway. I kappa B alpha is ubiquitinated in vivo and in vitro following phosphorylation, and mutations that abolish phosphorylation and degradation of I kappa B alpha in vivo prevent ubiquitination in vitro. Ubiquitinated I kappa B alpha remains associated with NF-kappa B, and the bound I kappa B alpha is degraded by the 26S proteasome. Thus, ubiquitination provides a mechanistic link between phosphorylation and degradation of I kappa B alpha.

Multi-step activation of NF-kappa B/Rel transcription factors

Transcription factors belonging to the NF-kappa B/Rel family are specialized in the transduction of primarily pathogenic signals from the cytoplasm to the cell nucleus. To date, the family comprises five distinct DNA-binding subunits and five regulatory proteins with inhibitory function, called I kappa B proteins. The interaction of dimers of the DNA-binding subunits with the I kappa B proteins leads to the cytoplasmatic retention of the complex and inhibition of its DNA binding. Following stimulation of cells, the I kappa B proteins become phosphorylated and are subsequently degraded, presumably, by the proteasome. The released NF-kappa B/Rel transcription factors can then enter the nucleus, bind to decameric DNA cognate sequences and stimulate transcription of numerous immunologically important target genes. In this article, we discuss several distinct levels at which the NF-kappa B/Rel transcription factors can be regulated.

Characterization of elements determining the dimerization properties of RelB and p50

Members of the Rel/NF-kappa B family of transcription factors share a region of approximately 300 amino acids which mediates dimerization and sequence-specific binding to DNA. Here we report a detailed characterization of the dimerization domain of RelB. The structural core sufficient to form stable Rel/NF-kappa B dimeric complexes consists of about 110 residues. The dimerization and DNA binding properties of more than 50 RelB mutants were analyzed by using p50 and p52 as partners. We present evidence that amino acids of a conserved element in the dimerization domain play a role in the recognition of a kappa B DNA target sequence. The analysis of hybrid molecules with dimerization domains containing different parts of p50 and RelB allowed us to identify some important structural elements determining homo- and heterodimerization properties. Furthermore, we were able to rescue the dimerization-defective mutant RelB-N287D by the introduction of a counteracting mutation intramolecularly (cis), and also intermolecularly (trans) by a mutation in the NF-kappa B dimerization partner p50. Correspondingly, a dimerization defective p50 mutant was effectively rescued by RelB-N287D.

Application of antisense technology to therapeutics

Antisense oligonucleotides inhibit gene expression by binding in a sequence-specific manner to an RNA target. Modern nucleotide chemistry has enabled the synthesis of chemically modified oligonucleotides that are highly resistant to nuclease degradation. Among other applications, these agents are currently being evaluated as potential antiviral and anticancer drugs. However, several unsolved problems remain. Poor efficiency of delivery to cells, tissue toxicity and antisense-independent biological effects of oligonucleotides currently limit the widespread application of antisense oligonucleotides to human disease. This article reviews some of the applications of antisense oligonucleotides and discusses problems associated with these applications.

Isolation of two new members of the NF-AT gene family and functional characterization of the NF-AT proteins

The activation of cytokine genes in response to antigenic stimulation of T cells is mediated by NF-AT proteins. Previous studies have identified two NF-AT proteins, NF-ATp and NF-ATc, that are homologous within a 290 aa domain distantly related to the Rel domain. We have isolated two additional members of this gene family, NF-AT3 and NF-AT4, which encode proteins 65% identical to the other NF-AT proteins within the Rel domain. The four NF-AT genes are transcribed in different sets of tissues that included many sites of expression outside the immune system. The Rel homology domain is sufficient for DNA recognition and cooperative binding interactions with AP-1. Although other members of the Rel family bind DNA as dimers, NF-AT proteins are monomers in solution or bound to DNA. Transfection assays indicate that each of the four NF-AT proteins can activate the IL-2 promoter in T cells.

A STAT protein domain that determines DNA sequence recognition suggests a novel DNA-binding domain

Stat1 and Stat3 are two members of the ligand-activated transcription factor family that serve the dual functions of signal transducers and activators of transcription. Whereas the two proteins select very similar (not identical) optimum binding sites from random oligonucleotides, differences in their binding affinity were readily apparent with natural STAT-binding sites. To take advantage of these different affinities, chimeric Stat1:Stat3 molecules were used to locate the amino acids that could discriminate a general binding site from a specific binding site. The amino acids between residues approximately 400 and approximately 500 of these approximately 750-amino-acid-long proteins determine the DNA-binding site specificity. Mutations within this region result in Stat proteins that are activated normally by tyrosine phosphorylation and that dimerize but have greatly reduced DNA-binding affinities.

Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NF kappa B

BACKGROUND

Human thioredoxin is a 12 kDa cellular redox protein that plays a key role in maintaining the redox environment of the cell. It has recently been shown to be responsible for activating the DNA-binding properties of the cellular transcription factor, NF kappa B, by reducing a disulfide bond involving Cys62 of the p50 subunit. Using multidimensional heteronuclear-edited and hetero-nuclear-filtered NMR spectroscopy, we have solved the solution structure of a complex of human thioredoxin and a 13-residue peptide extending from residues 56-68 of p50, representing a kinetically stable mixed disulfide intermediate along the reaction pathway.

RESULTS

The NF kappa B peptide is located in a long boot-shaped cleft on the surface of human thioredoxin delineated by the active-site loop, helices alpha 2, alpha 3 and alpha 4, and strands beta 3 and beta 4. The peptide adopts a crescent-like conformation with a smooth 110 degrees bend centered around residue 60 which permits it to follow the path of the cleft.

CONCLUSIONS

In addition to the intermolecular disulfide bridge between Cys32 of human thioredoxin and Cys62 of the peptide, the complex is stabilized by numerous hydrogen-bonding, electrostatic and hydrophobic interactions which involve residues 57-65 of the NF kappa B peptide and confer substrate specificity. These structural features permit one to suggest the specificity requirements for human thioredoxin-catalyzed disulfide bond reduction of proteins.

Structure of the NF-kappa B transcription factor: a holistic interaction with DNA

An unexpected mode of binding to DNA is revealed in two crystal structures of a transcription factor that is essential for many signalling pathways in eukaryotic cells.

Structure of NF-kappa B p50 homodimer bound to a kappa B site

The 2.3-A crystal structure of the transcription factor NK-kappa B p50 homodimer bound to a palindromic kappa B site reveals that the Rel homology region folds into two distinct domains, similar to those in the immunoglobulin superfamily. The p50 dimer envelopes an undistorted B-DNA helix, making specific contacts along the 10-base-pair kappa B recognition site mainly through loops connecting secondary structure elements in both domains. The carboxy-terminal domains form a dimerization interface between beta-sheets using residues that are strongly conserved in the Rel family.