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PAS domains: internal sensors of oxygen, redox potential, and light.

PAS domains are newly recognized signaling domains that are widely distributed in proteins from members of the Archaea and Bacteria and from fungi, plants, insects, and vertebrates. They function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. Specificity in sensing arises, in part, from different cofactors that may be associated with the PAS fold. Transduction of redox signals may be a common mechanistic theme in many different PAS domains. PAS proteins are always located intracellularly but may monitor the external as well as the internal environment. One way in which prokaryotic PAS proteins sense the environment is by detecting changes in the electron transport system. This serves as an early warning system for any reduction in cellular energy levels. Human PAS proteins include hypoxia-inducible factors and voltage-sensitive ion channels; other PAS proteins are integral components of circadian clocks. Although PAS domains were only recently identified, the signaling functions with which they are associated have long been recognized as fundamental properties of living cells.

Amino Acid Sequence↗

Effect of overexpressing the transcription factor E2F2 on cell cycle progression in rabbit corneal endothelial cells.

PURPOSE: To test the hypothesis that overexpression of the transcription factor E2F2 promotes cell cycle progression in nonproliferating corneal endothelial cells. METHODS: Ex vivo rabbit corneas were transfected with a lipid transfection reagent and either a control plasmid containing full-length cDNA for enhanced green fluorescent protein (pIRES2-EGFP) or a plasmid containing full-length cDNA for both E2F2 and EGFP (pIRES2-E2F2/EGFP). Transfection control experiments consisted of corneas incubated in buffer without transfection reagent or plasmid or incubated in reagent without plasmid. After transfection, corneas were incubated for various periods in 0.1% FBS (a concentration that maintains cell health, but does not promote proliferation). Immunocytochemical (ICC) localization tested for overexpression of E2F2 in transfected corneal endothelial cells and permitted calculation of transfection efficiency. Endothelial cell viability was tested in transfected ex vivo corneas and confluent cultures by using a cell-viability assay. Apoptosis was detected in confluent cultures by TUNEL assay. RT-PCR tested for mRNA expression of Ki67 (a marker of actively cycling cells) and cyclin B1 (a marker for the G2-phase of the cell cycle). Semiquantitative densitometric analysis compared the relative amounts of PCR reaction products. RESULTS: ICC demonstrated the colocalization of E2F2 and EGFP in corneal endothelium with a transfection efficiency of 10% to 12%, using the pIRES2-based plasmid and transfection reagent. The cell-viability assay revealed very few dead cells in ex vivo corneal endothelium that overexpressed E2F2. Cell viability and TUNEL assays of confluent cultures revealed that approximately 27% of cells died in all cultures incubated with transfection reagent, but death appeared not to be due to apoptosis. No additional cell death was noted by either assay in cells that overexpressed E2F2. RT-PCR of endothelial samples obtained 48 hours after transfection showed the presence of higher levels of reaction product for Ki67 (a 5.1-fold increase) and cyclin B1 (a 2.3-fold increase) in cells that overexpressed E2F2 than in control samples. CONCLUSIONS: Overexpression of the transcription factor E2F2 in nonproliferating rabbit corneal endothelial cells induces cell cycle progression without inducing significant apoptosis.

Animals↗

The age-related decrease in E47 DNA-binding does not depend on increased Id inhibitory proteins in bone marrow-derived B cell precursors.

Our previous results showed that decreased numbers of pre-B cells in aged mice were associated with decreases in surrogate light chain, lambda5, and transcription factors E47/E12. In the present paper, we have analyzed IL-7-expanded populations of pro-B/early pre-B cells to evaluate whether the age-related reduction in E47 DNA-binding could be attributed to reduced E47 expression and/or increased Id expression. According to the percentage of pre-B cells present in their bone marrow, old mice were classified as severely depleted (>80% loss in pre-B cells, 50% loss in pro-B cells), or moderately depleted (20-80% loss in pre-B cells). Results herein show that IL-7-stimulated pro-B/pre-B cells from both severely depleted and moderately depleted old mice exhibit a reduced E47 DNA-binding capacity compared to young mice, and this defect in severely depleted old mice is more dramatic than that in moderately depleted old mice. Id proteins, which are inhibitors of E47, are not increased in nuclear extracts of IL-7-expanded pro-B/early pre-B cells from severely depleted or moderately depleted old mice. We therefore conclude that the reduced expression of E47 protein alone in severely depleted and to a lesser extent in moderately depleted old mice explains the reduced amount of E47-DNA binding.

Age Factors↗

c-Myc trans-activates the p53 promoter through a required downstream CACGTG motif.

c-Myc and wild-type p53 have been shown to play important roles in the regulation of cellular proliferation and oncogenic transformation. We have previously shown that the p53 promoter contains a conserved consensus recognition sequence for the basic-helix-loop-helix-containing proteins, identical to the specific binding site for c-Myc/Max heterodimers. Here, we demonstrate that this element, which is required for full promoter activity, is bound by in vitro translated c-Myc/Max heterodimers. Furthermore, we found that in cotransfection assays, c-Myc trans-activates the p53 promoter as well as a hybrid herpes simplex virus-thymidine kinase promoter containing multiple copies of a synthetic p53-derived c-Myc binding site. The p53 promoter deleted of the basic-helix-loop-helix consensus recognition sequence is not trans-activated by c-Myc, thus suggesting that c-Myc trans-activates the p53 promoter through the basic-helix-loop-helix recognition motif. These findings raise the possibility that the p53 gene may be a potential target for trans-activation by c-Myc in vivo.

Animals↗

Functional dissection of the Drosophila enhancer of split protein, a suppressor of neurogenesis.

The Enhancer of split [E(spl)] gene complex of Drosophila comprises seven related genes encoding a special type of basic helix-loop-helix proteins, the function of which is to suppress the neural developmental fate. One of these proteins is E(spl) itself. To gain insight into the structural requirements for E(spl) function, we have expressed a large number of deletion variants in transgenic flies. Three protein domains were identified as essential for suppression of bristle development: the carboxyl-terminal tetrapeptide WRPW, the region comprising the putative helix III and helix IV, and the region between helix IV and the WRPW motif. Lack of the basic helix-loop-helix domain, helix III or IV, only partially inhibits the suppressor activity of the protein. Truncated variants that lack all the regions carboxyl-terminal to helix IV elicit the development of additional neural progenitors, and thus act as dominant-negative variants. All these results suggest that E(spl) suppresses neural development by direct interaction with other proteins, such as groucho and the proneural proteins.

Animals↗

XCoe2, a transcription factor of the Col/Olf-1/EBF family involved in the specification of primary neurons in Xenopus.

BACKGROUND: Primary neurogenesis in Xenopus is a model for studying the control of neural cell fate decisions. The specification of primary neurons appears to be driven by transcription factors containing a basic region and a helix-loop-helix (HLH) motif: expression of Xenopus neurogenin-related-1 (X-ngnr-1) defines the three prospective domains of primary neurogenesis, and expression of XNeuroD coincides with neuronal differentiation. The transition between neuronal competence and stable commitment to a neuronal fate remains poorly characterised, however. RESULTS: Drosophila Collier and rodent early B-cell factor/olfactory-1 define a family of HLH transcription factors containing a previously unknown type of DNA-binding domain. We isolated an orthologous gene from Xenopus, Xcoe2, which is expressed in precursors of primary neurons. Xcoe2 is transcribed after X-ngnr-1 and before XNeuroD. Overexpression of a dominant-negative mutant of XCoe2 prevented neuronal differentiation. Conversely, overexpressed wild-type Xcoe2 could promote ectopic differentiation of neurons, in both the neural plate and the epidermis. In contrast to studies with X-ngnr-1 or XNeuroD, the supernumerary neurons induced by Xcoe2 appeared in a 'salt-and-pepper' pattern, resulting from the activation of X-Delta1 expression and feedback regulation by lateral inhibition. CONCLUSIONS: XCoe2 may play a pivotal role in the transcriptional cascade that specifies primary neurons in Xenopus embryos: by maintaining Delta-Notch signalling, XCoe2 stabilises the higher neural potential of selected progenitor cells that express X-ngnr-1, ensuring the transition between neural competence and irreversible commitment to a neural fate; and it promotes neuronal differentiation by activating XNeuroD expression, directly or indirectly.

Amino Acid Sequence↗

Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme.

The hairpin ribozyme is a naturally occurring catalytic RNA composed of two helix-loop-helix domains, A and B, that dock to form the biologically active enzyme. Previously, the crystal structure of the hairpin has been solved as a four-way helical junction that incorporated the U1A protein as an artificial crystal-packing motif [Rupert & Ferré-D'Amaré (2001), Nature (London), 410, 780-786]. Here, the crystallization of a minimal junctionless hairpin ribozyme 64-mer is reported in the absence of protein. Crystals grow in space group P6(1)22, with unit-cell parameters a = 93.1, c = 123.2 A. Complete diffraction data have been collected to 3.35 A resolution. Structural analysis should provide details of intermolecular RNA docking, including the ground-state conformations of the U(39)C mutation relevant to hairpin catalysis.

Base Sequence↗

The secondary structure of the ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein.

The ets family of eukaryotic transcription factors is characterized by a conserved DNA-binding domain of approximately 85 amino acids for which the three-dimensional structure is not known. By using multidimensional NMR spectroscopy, we have determined the secondary structure of the ets domain of one member of this gene family, human Fli-1, both in the free form and in a complex with a 16-bp cognate DNA site. The secondary structure of the Fli-1 ets domain consists of three alpha-helices and a short four-stranded antiparallel beta-sheet. This secondary structure arrangement resembles that of the DNA-binding domain of the catabolite gene activator protein of Escherichia coli, as well as those of several eukaryotic DNA-binding proteins including histone H5, HNF-3/fork head, and the heat shock transcription factor. Differences in chemical shifts of backbone resonances and amide exchange rates between the DNA-bound and free forms of the Fli-1 ets domain suggest that the third helix is the DNA recognition helix, as in the catabolite gene activator protein and other structurally related proteins. These results suggest that the ets domain is structurally similar to the catabolite gene activator protein family of helix-turn-helix DNA-binding proteins.

Amino Acid Sequence↗

Palindromic Haemophilus DNA uptake sequences in presumed transcriptional terminators from H. influenzae and H. parainfluenzae.

We have found palindromic pairs of near matches to the 11-bp Haemophilus DNA uptake motif shortly after the stop codons of three Haemophilus genes. Short runs of thymidylate residues follow the stem-loop structures thus defined. This organization suggests that, in H. influenzae, the uptake motif may be preferentially incorporated into gene termination signals, as has been proposed for Neisseria gonorrhoeae.

Base Sequence↗

Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1.

Bacterial release factor RF2 promotes termination of protein synthesis, specifically recognizing stop codons UAA or UGA. The crystal structure of Escherichia coli RF2 has been determined to a resolution of 1.8 A. RF2 is structurally distinct from its eukaryotic counterpart eRF1. The tripeptide SPF motif, thought to confer RF2 stop codon specificity, and the universally conserved GGQ motif, proposed to be involved with the peptidyl transferase center, are exposed in loops only 23 A apart, and the structure suggests that stop signal recognition is more complex than generally believed.

Amino Acid Sequence↗

Crucial role of the residue R280 at the F'-G' loop of the human granulocyte/macrophage colony-stimulating factor receptor alpha chain for ligand recognition.

The receptor for granulocyte/macrophage colony-stimulating factor (GM-CSF) is composed of two chains, alpha and betac. Both chains belong to the superfamily of cytokine receptors characterized by a common structural feature, i.e., the presence of at least two fibronectin-like folds in the extracellular domain, which was first identified in the growth hormone receptor. The GM-CSF receptor (GMR)-alpha chain confers low affinity binding only (5-10 nM), whereas the other chain, betac, does not bind GM-CSF by itself but confers high affinity binding when associated with GMR-alpha (25-100 pM). The present study was designed to define the assembly of the GMR complex at the molecular level through site-directed mutagenesis guided by homology modeling with the growth hormone receptor complex. In our three-dimensional model, R280 of GMR-alpha, located in the F'-G' loop and close to the WSSWS motif, is in the vicinity of the ligand Asp112, suggesting the possibility of electrostatic interaction between these two residues. Through site directed mutagenesis, we provide several lines of evidence indicating the importance of electrostatic interaction in ligand-receptor recognition. First, mutagenesis of GMR-alphaR280 strikingly ablated ligand binding in the absence of beta common (betac); ligand binding was restored in the presence of betac with, nonetheless, a significant shift from high (26 pM) toward low affinity (from 2 to 13 nM). The rank order of the dissociation constant for the different GMR-alphaR280 mutations where Lys > Gln > Met > Asp, suggesting the importance of the charge at this position. Second, a mutant GM-CSF with charge reversal mutation at position Asp112 exhibited a 1,000-fold decrease in affinity in receptor binding, whereas charge ablation or conservative mutations were the least affected (10-20-fold). Third, removal of the charge at position R280 of GMR-alpha introduced a 10-fold decrease in the association rate constant and only a 2-fold change in the dissociation rate constant, suggesting that R280 is implicated in ligand recognition, possibly through interaction with Asp112 of GM-CSF. For all R280 mutants, the half-efficient concentrations of GM-CSF required for membrane (receptor binding) to nuclear events (c-fos promoter activation) and cell proliferation (thymidine incorporation) were in the same range, indicating that the threshold for biologic activity is governed mainly by the affinity of ligand-receptor interaction. Furthermore, mutation of other residues in the immediate vicinity of R280 was less drastic. Sequence alignment and modeling of interleukin (IL)-3R and IL-5R identified an arginine residue at the tip of a beta turn in a highly divergent context at the F'-G' loop, close to a conserved structural element, the WSXWS motif, suggesting the possibility of a ligand association mechanism similar to the one described herein for GMR.

3T3 Cells↗

Structure, chromosome mapping, and expression of the mouse Lyl-1 gene.

The mouse Lyl-1 gene was cloned and shown to consist of four exons with extensive nucleotide and structural homology to the human LYL1 gene. The Lyl-1 gene was localized to the central region of mouse chromosome 8 which defines a new region of synteny with human chromosome 19p. The predicted mouse Lyl-1 protein is 78% identical to human LYL1. The region of highest similarity occurs in the basic DNA binding and helix-loop-helix dimerization motifs which are nearly identical in mouse and man differing by only one conservative amino acid substitution. Expression of the Lyl-1 gene was found to be low in murine spleen and undetectable in other tissues by Northern blot analysis. In lymphoid cell lines, Lyl-1 was expressed in most B lineage cells but downregulated during terminal differentiation and was not expressed in most T lineage cells. In a human T ALL cell line carrying a translocation that juxtaposed LYL1 with the beta TCR gene, the translocated LYL1 gene was transcriptionally active whereas the nontranslocated gene was transcriptionally silent. We conclude that LYL1 has the properties of a lineage- and differentiation-specific HLH protein that contributes to T-cell neoplasia through its deregulated expression following chromosomal translocation.

Amino Acid Sequence↗

Helix-loop-helix motif in HIV-1 Rev.

Circular dichroism (CD) spectra of C-terminal deletion mutants of the HIV-1 Rev protein, Rev M9 delta 14 (missing aa 68-112) and Rev M11 delta 14 (lacking aa 92-112), indicated that Rev contains 46-49 residues in alpha-helical conformation within the N-terminal 71 or 95 amino acids of the 116 residue protein. Complexation with a 40-nucleotide fragment of the Rev responsive element, RRE, (G39 to C78), containing the minimal element for Rev binding, induced an A to B form structural transition in the RRE fragment, whereas the percentage of alpha-helical conformation in the protein stays constant on substrate binding. When complexed to the RNA, neither mutant protein showed structural changes upon raising the temperature to 40 degrees C, as determined by the lack of decrease of the signal intensity at 222 nm, indicative for alpha-helical conformation. In contrast, Rev M9 delta 14, which is shorter than Rev M11 delta 14 by 24 amino acids, in the absence of RNA, lost about 60% of the spectral minima at 222 nm at the same temperature. The Rev M11 delta 14 mutant, in the absence of RNA, showed a decrease of 20% in spectral intensity upon heating to 40 degrees C. Free and RNA-bound mutant proteins showed reversible transitions upon heating to 80 degrees C and subsequent cooling down to 10 degrees C overnight. The Rev peptide Cys 75-93, spanning the Rev transactivation domain, showed secondary structure in 40% and 60% hexafluoropropanol (HFP) solutions.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Solution structure of the Reps1 EH domain and characterization of its binding to NPF target sequences.

The recently described EH domain recognizes proteins containing Asn-Pro-Phe (NPF) sequences. Using nuclear magnetic resonance (NMR) data, we determined the solution structure of the EH domain from the Reps1 protein and characterized its binding to linear and cyclic peptides derived from a novel targeting protein. The structure calculation included 1143 distance restraints and 122 angle restraints and resulted in structures with a root-mean-square deviation of 0.40 +/- 0.05 A for backbone atoms of superimposed secondary structural elements. The structure comprises two helix-loop-helix motifs characteristic of EF-hand domains. Titration data with NPF-containing peptides showed evidence of intermediate exchange on the NMR chemical shift time scale, which required an analysis that includes curve fitting to obtain accurate equilibrium constants and dissociation rate constants. The cyclic and linear peptides bound with similar affinities (Kd = 65 +/- 17 and 46 +/- 14 microM, respectively) and to the same hydrophobic pocket formed between helices B and C. The cyclic peptide formed a complex that dissociated more slowly (k(off) = 440 +/- 110 s(-1)) than the linear peptide (k(off) = 1800 +/- 250 s(-1)), but had little change in affinity because of the slower rate of association of the cyclic peptide. In addition, we characterized binding to a peptide containing a DPF sequence (Kd = 0.5 +/- 0.2 mM). The characterization of binding between the Reps1 EH domain and its target proteins provides information about their role in endocytosis.

Adaptor Proteins, Signal Transducing↗

The helix-loop-helix gene E2A is required for B cell formation.

Heterodimers between tissue-specific basic-helix-loop-helix proteins and the gene products of E2A play major roles in determining tissue-specific cell fate. To understand the broad role of E2A in development, we have generated E2A mutant mice following homologous recombination in embryonic stem cells. Homozygous mutant mice develop to full term without apparent abnormalities, but then display a high rate of postnatal death. The surviving mice show retarded postnatal growth. Detailed examination of hematopoiesis reveals that the homozygous mutant mice contain no B cells while other lineages including T cell, granulocyte, macrophage, and erythroid are intact. The block to B cell differentiation occurs prior to immunoglobulin gene DH-JH rearrangement and the expression of the B lineage-specific marker B220. Surprisingly, heterozygous embryos contain, on average, about half as many B cells as wild-type embryos, suggesting the existence of a counting mechanism that translates levels of E2A into numbers of B cells.

Animals↗

Identification of residues involved in binding of IL5 to betacom using betaIL3 and betacom chimeras.

In mice there are two forms of the beta chain used in the IL3 receptor system, betacom and betaIL3. betacom is used by the IL3, IL5 and GM-CSF receptors whereas betaIL3 is only used in the IL3 receptor. In this work an assay was developed to identify residues of beta1L3 that restrict IL5 activity. It was found that such residues reside within the 2nd CRM of the molecule. Furthermore, when residues in the betaIL3 B'-C' loop were replaced with betacom sequence a form of betaIL3 was produced that was able to respond to IL5. This region is also responsible for IL3 binding to betaIL3 in the absence of alpha chain. It is therefore an important structural motif of betacom and betaIL3 responsible for both ligand interaction and specificity.

Amino Acid Sequence↗

'Loop' domain deletional mutant of Bcl-xL is as effective as p29Bcl-xL in inhibiting radiation-induced cytosolic accumulation of cytochrome c (cyt c), caspase-3 activity, and apoptosis.

PURPOSE/OBJECTIVE: To investigate the effect of the enforced expression of p29Bcl-xL or its loop deletional mutant, p18Bcl-xLdelta, on irradiation-induced apoptosis and cell-cycle distribution of HL-60 cells. MATERIALS & METHODS: We compared the irradiation-induced molecular cascade of apoptosis in control human AML HL-60/neo versus Bcl-xL overexpressing (approximately 8-fold) (HL-60/Bcl-xL) and HL-60/Bcl-XLdelta cells that express the loop domain deletional mutant construct (delta26-83 AA) of Bcl-xL. The three cell lines were irradiated with 6MV photons to varying doses up to 20 Gy. Following this, cytosolic cyt c levels, caspase-3 activity, and the Bcl-2 family of proteins were evaluated utilizing Western blot analysis (whole cell lysate or cytosolic S-100 fraction). Apoptosis was assessed by internucleosomal DNA fragmentation, Annexin-V staining and FACS analysis, as well as by morphologic criteria. The cell-cycle effects of radiation were analyzed by flow cytometry. RESULTS: Eight hours following irradiation (12 Gy) of HL-60/neo cells, a marked increase (approximately 8-fold) in the cytosolic accumulation of cyt c in the S-100 fraction was observed. This was associated with the cleavage of caspase-3, as well as the generation of its poly (ADP-ribose) polymerase (PARP) and DFF (DNA fragmentation factor)-45 cleavage activity. Twenty-four to forty-eight hours after irradiation, internucleosomal DNA fragmentation and positive Annexin-V staining (32.3+/-3.3%) was detected in HL-60/neo cells. In contrast, in both HL-60/Bcl-xL and HL-60/Bcl-xLdelta cells, a significantly lower percentage of apoptotic cells (p<0.05) were detected and internucleosomal DNA fragmentation was not induced. Following irradiation, Western analysis neither demonstrated any significant alteration in Bcl-2, p29Bcl-xL, p18Bcl-xLdelta, or Bax; nor induced CD95 (Fas receptor) or Fas ligand expression in any cell type. However, in all cell types, irradiation produced approximately a 2-fold increase in the percentage of cells in the G2/M phase of the cell cycle. CONCLUSION: These results demonstrate that an intact loop domain is not necessary for the full antiapoptotic function of Bcl-xL against irradiation-induced cytosolic accumulation of cyt c, caspase activation, and apoptosis of HL-60 cells. Additionally, the cell-cycle effects of ionizing radiation in HL-60 cells are not affected by enforced expression of Bcl-xL or Bcl-xLdelta.

Apoptosis↗

Id1 and Id3 are required for neurogenesis, angiogenesis and vascularization of tumour xenografts.

Id proteins may control cell differentiation by interfering with DNA binding of transcription factors. Here we show that targeted disruption of the dominant negative helix-loop-helix proteins Id1 and Id3 in mice results in premature withdrawal of neuroblasts from the cell cycle and expression of neural-specific differentiation markers. The Id1-Id3 double knockout mice also display vascular malformations in the forebrain and an absence of branching and sprouting of blood vessels into the neuroectoderm. As angiogenesis both in the brain and in tumours requires invasion of avascular tissue by endothelial cells, we examined the Id knockout mice for their ability to support the growth of tumour xenografts. Three different tumours failed to grow and/or metastasize in Id1+/- Id3-/- mice, and any tumour growth present showed poor vascularization and extensive necrosis. Thus, the Id genes are required to maintain the timing of neuronal differentiation in the embryo and invasiveness of the vasculature. Because the Id genes are expressed at very low levels in adults, they make attractive new targets for anti-angiogenic drug design.

Animals↗