A glucose-responsive transcription factor that regulates carbohydrate metabolism in the liver.

Carbohydrates mediate their conversion to triglycerides in the liver by promoting both rapid posttranslational activation of rate-limiting glycolytic and lipogenic enzymes and transcriptional induction of the genes encoding many of these same enzymes. The mechanism by which elevated carbohydrate levels affect transcription of these genes remains unknown. Here we report the purification and identification of a transcription factor that recognizes the carbohydrate response element (ChRE) within the promoter of the L-type pyruvate kinase (LPK) gene. The DNA-binding activity of this ChRE-binding protein (ChREBP) in rat livers is specifically induced by a high carbohydrate diet. ChREBP's DNA-binding specificity in vitro precisely correlates with promoter activity in vivo. Furthermore, forced ChREBP overexpression in primary hepatocytes activates transcription from the L-type Pyruvate kinase promoter in response to high glucose levels. The DNA-binding activity of ChREBP can be modulated in vitro by means of changes in its phosphorylation state, suggesting a possible mode of glucose-responsive regulation. ChREBP is likely critical for the optimal long-term storage of excess carbohydrates as fats, and may contribute to the imbalance between nutrient utilization and storage characteristic of obesity.

BSF binds specifically to the bicoid mRNA 3' untranslated region and contributes to stabilization of bicoid mRNA.

The early stages of Drosophila melanogaster development rely extensively on posttranscriptional forms of gene regulation. Deployment of the anterior body patterning morphogen, the Bicoid protein, requires both localization and translational regulation of the maternal bicoid mRNA. Here we provide evidence that the bicoid mRNA is also selectively stabilized during oogenesis. We identify and isolate a protein, BSF, that binds specifically to IV/V RNA, a minimal form of the bicoid mRNA 3' untranslated region that supports a normal program of mRNA localization during oogenesis. Mutations that disrupt the BSF binding site in IV/V RNA or substantially reduce the level of BSF protein lead to reduction in IV/V RNA levels, indicating a role for BSF in RNA stabilization. The BSF protein is novel and lacks all of the characterized RNA binding motifs. However, BSF does include multiple copies of the PPR motif, whose function is unknown but appears in other proteins with roles in RNA metabolism.

IL-1H, an interleukin 1-related protein that binds IL-18 receptor/IL-1Rrp.

IL-18, or IGIF (interferon-gamma inducing factor), is an IL-1-related, pro-inflammatory cytokine, which plays a pivotal role in systemic and local inflammation. We have identified and characterized IL-1H, a novel IL-1-related molecule. IL-1H appears to be expressed in most tissues with relatively high levels in testis, thymus and uterus. The IL-1H transcripts were stimulated by phorbol ester (PMA) in human cell lines (A431, THP-1 and KG-1) and peripheral blood mononuclear cells (HPBMC) and dendritic cells (NHDC). The protein sequence of IL-1H is mostly related to IL-1ra with a similarity of 36%. A short form of IL-1H was identified, and lacks a 40-amino acid segment in the amino-terminal region of the protein. When expressed in mammalian cells, two secreted polypeptides of IL-1H were identified: an uncleaved and a cleaved form starting with amino acid Val-46. Furthermore, IL-1H binds the IL-18 receptor, but not the IL-1 receptor. These findings suggest that IL-1H may be another ligand for the IL-18 receptor and a new player in the inflammatory and immune responses mediated by the IL-18/IL-18R axis.

Matrix-assisted laser desorption/ionization time-of-flight mass analysis of peptides.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is one of the most useful techniques for determining the mass of biomolecules, with exceptional capabilities for mass analysis of peptides. Relative to other ionization techniques, it provides high sensitivity and excellent tolerance of salt and other common buffer components. Routine detection limits for peptides are in the subpicomole range. The ions commonly observed are the protonated molecules (M+H(+)), which makes data analysis relatively easy. This overview discusses instrument configuration and calibration, sample preparation, along with specific approaches for analyzing peptide mixtures, synthetic peptides, and chemical modifications of peptides.

Reversed-phase isolation of peptides.

In reversed-phase HPLC, peptides are separated on a hydrophobic stationary phase and eluted with a gradient of increasing organic solvent concentration. Protocols describing the separation of peptides in 5- to 500-pmol quantities via narrow-bore (2-mm-i.d.) or microbore (1-mm-i.d.) columns, as well as for the separation of peptides in quantities <5 pmol are provided in this unit. Capillary HPLC columns require a gradient flow rate of 3 to 5 omponents present in a small sample prior to automated sequencing is possible via the procedures for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and capillary electrophoresis.

The Rela(p65) subunit of NF-kappaB is essential for inhibiting double-stranded RNA-induced cytotoxicity.

Double-stranded RNA (dsRNA) molecules generated during virus infection can initiate a host antiviral response to limit further infection. Such a response involves induction of antiviral gene expression by the dsRNA-activated protein kinase (PKR) and the NF-kappaB transcription factor. In addition, dsRNA can also induce apoptosis by an incompletely understood mechanism that may serve to further limit viral replication. Here we demonstrate a novel role for the RelA subunit of NF-kappaB in inhibiting dsRNA-induced cell death. dsRNA treatment resulted in caspase 3 activation and apoptotic morphological transformations in mouse embryonic fibroblasts (MEFs) derived from RelA-/- mice but not from RelA+/+ mice. Such dsRNA-induced killing could be inhibited by expression of either a dominant-negative mutant of PKR or wild-type RelA. Interestingly, caspase 3 activated following dsRNA treatment of RelA-/- MEFs was essential for apoptotic nuclear changes but dispensable for cytotoxicity. A broader specificity caspase inhibitor was also unable to inhibit dsRNA-induced cytotoxicity, suggesting that caspase activation is not essential for the induction of cell death by dsRNA in MEFs. However, combined inhibition of caspase 3 and reactive oxygen species production resulted in complete inhibition of dsRNA-induced cytotoxicity. These results demonstrate an essential role for NF-kappaB in protecting cells from dsRNA-induced apoptosis and suggest that NF-kappaB may inhibit both caspase-dependent and reactive oxygen species-dependent cytotoxic pathways.

Cleavage and identification of proteins: a modified aspartyl-prolyl cleavage.

We have developed a method for rapidly cleaving and identifying proteins electroblotted onto poly(vinylidene difluoride) membranes. Cleavage is performed with 10% acetic acid in 7 M guanidine chloride at pH 2.5 for 1 h at 90 degrees C, resulting in fragmentation primarily at aspartyl-prolyl bonds. Peptides resulting from non-Asp-Pro cleavage are N-terminally blocked by reaction with orthophthalaldehyde (OPA) prior to automated Edman degradation. Reaction with OPA after cleavage blocks all amino acids containing primary amino groups. Only peptides containing an N-terminal amino acid with a secondary amino group (proline) will be available for reaction with the Edman reagent. The sequences obtained are used for protein database searching. Using this approach, proteins that are found to be N-terminally blocked can be removed from the sequencer, cleaved with acetic acid, blocked with OPA, and reapplied to the sequencer. The protein can then be identified from a database search using the sequence mixture obtained.

Deficiency of T2K leads to apoptotic liver degeneration and impaired NF-kappaB-dependent gene transcription.

Induction of NF-kappaB-dependent transcription requires phosphorylation and subsequent degradation of I-kappaB, an inhibitor of NF-kappaB, followed by nuclear translocation and DNA binding of NF-kappaB. Tumor necrosis factor receptor-associated factor 2 (TRAF2) plays a role in NF-kappaB activation in response to cytokines such as tumor necrosis factor alpha (TNFalpha). In this study, we purified and characterized a novel kinase (T2K, also known as TBK1 or NAK), which associates with TRAF2 and exhibits kinase activity towards I-kappaBalpha in vitro. The physiological function of T2K was investigated using T2K-deficient mice. Heterozygotes appear normal, but t2k(-/-) animals die at approximately E14.5 of massive liver degeneration and apoptosis. Never theless, hematopoietic progenitors from T2K-deficient fetal liver support normal lymphocyte development. Furthermore, t2k(-/-) embryonic fibroblasts and thymocytes do not display increased sensitivity to TNFalpha-induced apoptosis. In response to either TNFalpha or IL-1 induction, t2k(-/-) embryonic fibroblasts exhibit normal degradation of I-kappaB and kappaB-binding activity. However, NF-kappaB-directed transcription is dramatically reduced. These results demonstrate that, like I-kappaB kinase beta and the RelA subunit of NF-kappaB, T2K is critical in protecting embryonic liver from apoptosis. However, T2K has a unique role in the activation of NF-kappaB-directed transcription, apparently independent of I-kappaB degradation and NF-kappaB DNA binding.

FIZZ1, a novel cysteine-rich secreted protein associated with pulmonary inflammation, defines a new gene family.

Bronchoalveolar lavage fluid from mice with experimentally induced allergic pulmonary inflammation contains a novel 9.4 kDa cysteine-rich secreted protein, FIZZ1 (found in inflammatory zone). Murine (m) FIZZ1 is the founding member of a new gene family including two other murine genes expressed, respectively, in intestinal crypt epithelium and white adipose tissue, and two related human genes. In control mice, FIZZ1 mRNA and protein expression occur at low levels in a subset of bronchial epithelial cells and in non-neuronal cells adjacent to neurovascular bundles in the peribronchial stroma, and in the wall of the large and small bowel. During allergic pulmonary inflammation, mFIZZ1 expression markedly increases in hypertrophic, hyperplastic bronchial epithelium and appears in type II alveolar pneumocytes. In vitro, recombinant mFIZZ1 inhibits the nerve growth factor (NGF)-mediated survival of rat embryonic day 14 dorsal root ganglion (DRG) neurons and NGF-induced CGRP gene expression in adult rat DRG neurons. In vivo, FIZZ1 may modulate the function of neurons innervating the bronchial tree, thereby altering the local tissue response to allergic pulmonary inflammation.

Simian virus 40 large T antigen binds a novel Bcl-2 homology domain 3-containing proapoptosis protein in the cytoplasm.

A 193-kDa SV40 large T antigen (T-Ag)-binding protein, designated p193, was identified and cloned. Inspection of the deduced amino acid sequence revealed the presence of a short motif similar to the Bcl-2 homology (BH) domain 3, suggesting that p193 may be a member of a family of apoptosis promoting proteins containing only BH3 motifs. In support of this, p193 expression promoted apoptosis in NIH-3T3 cells. Deletion of the BH3 motif abolished p193 apoptosis activity. p193-induced apoptosis was antagonized by co-expression of Bcl-X(L). Immune cytologic analysis indicated that p193 is localized to the cytoplasm of transfected cells. p193-induced apoptosis was also antagonized by co-expression of T-Ag, which resulted in the cytoplasmic localization of both proteins. The p193 binding site was mapped to an N-terminal region of T-Ag previously implicated in transforming activity. These results suggest that T-Ag possesses an antiapoptosis activity, independent of p53 sequestration, which is actuated by T-Ag/p193 binding in the cytoplasm.

ABRF-98SEQ: Evaluation of peptide sequencing at high sensitivity.

The ABRF-98SEQ sample was the 11th in a series of amino acid sequencing studies performed by the Protein Sequence Research Group of the Association of Biomolecular Resource Facilities. This study was designed to aid participants' laboratories in determining their abilities to analyze the amino acid sequence of a peptide at high sensitivity using Edman degradation, mass spectrometry (MS), or both. ABRF-98SEQ is a 17-amino acid synthetic peptide (IFDDEIEEVQALYPTER) that resembles a typical tryptic peptide. It was distributed at the 2.8-pmol level. The sample was sent dried in a microfuge tube accompanied by instructions on solubilizing the sample and by a survey form. Including tentative calls, the correct sequence was obtained by 16% of the responding participants, compared with only 6% in the 1997 study when the low-level peptide was a minor component of a mixture. This increase probably reflects the purity of ABRF-98SEQ. A secondary factor in the increase in correct calls may be the larger number of respondents this year reporting that they perform sequence analysis at the 1- to 10-pmol level. Most respondents who obtained the correct sequence used a combination of Edman sequencing and molecular weight determination by MS. Overall, the accuracy and sensitivity of peptide sequencing by Edman degradation continue to improve and are clearly aided by the use of MS for molecular weight determination. Although peptide sequencing by MS is not yet routinely practiced by the participating laboratories, results of this study indicate that MS-derived sequence data, when properly interpreted, are valuable for correcting, completing, or corroborating sequence assignments derived by Edman.

Purification and characterization of a novel 35-kDa protein from transformed cardiomyocytes.

A 35-kDa protein (designated p35) showing antigenic homology with an N-terminal epitope on the SV-40 large T-antigen oncoprotein was purified from transformed cardiomyocytes. Sequence analysis of several tryptic peptides indicated that p35 was not homologous to previously described sequences. Polyclonal antibody raised against synthetic peptide containing one of the tryptic fragments was used in Western blot analyses to ascertain the tissue-specific pattern of p35 expression. p35 was expressed ubiquitously in adult mouse tissues, and was detected in both embryonic and transformed cardiomyocyte preparations. Subcellular fractionation studies indicated that p35 is an integral membrane protein. Expression of p35 appeared to be regulated by growth conditions as evidenced by a transient decrease in protein levels following the addition of serum to quiescent NIH 3T3 cells.

Smaug, a novel and conserved protein, contributes to repression of nanos mRNA translation in vitro.

Proper deployment of Nanos protein at the posterior of the Drosophila embryo, where it directs posterior development, requires a combination of RNA localization and translational controls. These controls ensure that only the posteriorly-localized nanos mRNA is translated, whereas unlocalized nanos mRNA is translationally repressed. Here we describe cloning of the gene encoding Smaug, an RNA-binding protein that interacts with the sequences, SREs, in the nanos mRNA that mediate translational repression. Using an in vitro translation assay, we demonstrate that SRE-dependent repression occurs in extracts from early stage embryos. Immunodepletion of Smaug from the extracts eliminates repression, consistent with the notion that Smaug is involved. Smaug is a novel gene and the existence of potential mammalian Smaug homologs raises the possibility that Smaug represents a new class of conserved translational repressor.

Receptor binding and biological activity of mammalian expressed sensory and motor neuron-derived factor (SMDF).

Sensory and motor neuron-derived factor (SMDF) is a member of the neuregulin family of proteins. SMDF is structurally characterized by a novel N-terminal domain. Using the signal sequence and N-terminal 28 amino acids (the "epitope") of herpes simplex virus type 1 glycoprotein D (gD), we have expressed SMDF as an epitope-tagged protein (gD-SMDF) in 293 cells, and purified it to > 98% homogeneity on a monoclonal anti-gD column. gD-SMDF stimulates human Schwann cell growth and 3H-thymidine incorporation in MCF-7 and T47D human breast tumor cells in vitro. The biological activity of gD-SMDF is consistent with its ability to compete with 125I-labeled heregulinbeta1 peptide (rHRGbeta1(177-244)) to bind to soluble dimeric ErbB receptor-IgG fusion proteins. gD-SMDF binds with low affinity to homodimeric ErbB3-IgG and ErbB4-IgG but with higher affinity to heterodimeric ErbB2/ErbB3-IgG and ErbB2/ErbB4-IgG. Using a SMDF-IgG(Fc) fusion protein we generated a monoclonal antibody (3G11) which binds SMDF, crossreacts with rHRGbeta1(177-244), and neutralizes the in vitro activities of gD-SMDF and rHRGbeta1(177-244) in human Schwann cells.

A two-dimensional protein map of Chinese hamster ovary cells.

Chinese hamster ovary (CHO) cells are used extensively for the expression of biopharmaceutical protein products. As part of our effort to better understand CHO cell physiology and protein expression changes caused by modified culture conditions, we have begun to map CHO cell polypeptides. A parental cell line reference map was established using two-dimensional gel electrophoresis with immobilized pH gradients (pH 3-10) in the first dimension and a linear acrylamide gradient (9-18%T) in the second dimension. The map is composed of over 1000 silver-stained protein spots. Protein identification is proceeding using a combination of immunostaining, NH2-terminal sequencing, and mass spectrometric analyses. Among the proteins so far identified are glucose-regulated protein 78 (GRP78), protein disulfide isomerase (PDI), galectin-1, and several heat-shock proteins. The goal is to generate a database which emphasizes those proteins most relevant to the use of CHO cells as a host for recombinant protein expression.

Biochemical purification of a mammalian slit protein as a positive regulator of sensory axon elongation and branching.

Many neurons in both vertebrates and invertebrates innervate multiple targets by sprouting secondary axon collaterals (or branches) from a primary axon shaft. To begin to identify molecular regulators of axon branch initiation or extension, we studied the growth of single sensory axons in an in vitro collagen assay system and identified an activity in extracts of embryonic spinal cord and of postnatal and adult brain that promotes the elongation and formation of extensive branches by these axons. Biochemical purification of the activity from calf brain extracts led to the identification of an amino-terminal fragment of Slit2 as the main active component and to the discovery of a distinct activity that potentiates its effects. These results indicate that Slit proteins may function as positive regulators of axon collateral formation during the establishment or remodeling of neural circuits.

Slit proteins bind Robo receptors and have an evolutionarily conserved role in repulsive axon guidance.

Extending axons in the developing nervous system are guided in part by repulsive cues. Genetic analysis in Drosophila, reported in a companion to this paper, identifies the Slit protein as a candidate ligand for the repulsive guidance receptor Roundabout (Robo). Here we describe the characterization of three mammalian Slit homologs and show that the Drosophila Slit protein and at least one of the mammalian Slit proteins, Slit2, are proteolytically processed and show specific, high-affinity binding to Robo proteins. Furthermore, recombinant Slit2 can repel embryonic spinal motor axons in cell culture. These results support the hypothesis that Slit proteins have an evolutionarily conserved role in axon guidance as repulsive ligands for Robo receptors.

Involvement of regulatory and catalytic subunits of phosphoinositide 3-kinase in NF-kappaB activation.

Hypoxia, reoxygenation, and the tyrosine phosphatase inhibitor pervanadate activate the transcription factor NF-kappaB, involving phosphorylation of its inhibitor IkappaB-alpha on tyrosine 42. This modification does not lead to degradation of IkappaB by the proteasome/ubiquitin pathway, as is seen on stimulation of cells with proinflammatory cytokines. It is currently unknown how tyrosine-phosphorylated IkappaB is removed from NF-kappaB. Here we show that p85alpha, the regulatory subunit of PI3-kinase, specifically associates through its Src homology 2 domains with tyrosine-phosphorylated IkappaB-alpha in vitro and in vivo after stimulation of T cells with pervanadate. This association could provide a mechanism by which newly tyrosine-phosphorylated IkappaB is sequestered from NF-kappaB. Another mechanism by which PI3-kinase contributed to NF-kappaB activation in response to pervanadate appeared to involve its catalytic p110 subunit. This was evident from the inhibition of pervanadate-induced NF-kappaB activation and reporter gene induction by treatment of cells with nanomolar amounts of the PI3-kinase inhibitor wortmannin. The compound had virtually no effect on tumor necrosis factor- and interleukin-1-induced NF-kappaB activities. Wortmannin did not inhibit tyrosine phosphorylation of IkappaB-alpha or alter the stability of the PI3-kinase complex but inhibited Akt kinase activation in response to pervanadate. Our data suggest that both the regulatory and the catalytic subunit of PI3-kinase play a role in NF-kappaB activation by the tyrosine phosphorylation-dependent pathway.

Protein identification using 20-minute Edman cycles and sequence mixture analysis.

We have developed a 20-min Edman cycle and a multiple sample horizontal flow reactor for the sequence analysis of PVDF-electroblotted proteins. The 20-min cycle uses a 12-min C18 phenylthiohydantoin separation. This cycle and separation is compatible with most Applied Biosystems sequencers. Using this rapid cycle, 10 residues on six different proteins can be completed within a 24-h period. We also demonstrate the use of an algorithm that can sort mixture sequences derived from PVDF bands that contain coeluting proteins.

Scythe: a novel reaper-binding apoptotic regulator.

Reaper is a central regulator of apoptosis in Drosophila melanogaster. With no obvious catalytic activity or homology to other known apoptotic regulators, reaper's mechanism of action has been obscure. We recently reported that recombinant Drosophila reaper protein induced rapid mitochondrial cytochrome c release, caspase activation and apoptotic nuclear fragmentation in extracts of Xenopus eggs. We now report the purification of a 150 kDa reaper-interacting protein from Xenopus egg extracts, which we have named Scythe. Scythe is highly conserved among vertebrates and contains a ubiquitin-like domain near its N-terminus. Immunodepletion of Scythe from extracts completely prevented reaper-induced apoptosis without affecting apoptosis triggered by activated caspases. Moreover, a truncated variant of Scythe lacking the N-terminal domain induced apoptosis even in the absence of reaper. These data suggest that Scythe is a novel apoptotic regulator that is an essential component in the pathway of reaper-induced apoptosis.