A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing

An efficient approach for structural studies on bacterial chromosomes is presented. It is based on high-resolution PCR map construction by using a multiplex long accurate PCR (MLA PCR) protocol and a YAC clone carrying the region to be mapped as indicator. The high-resolution PCR map of the bacillus subtilis rrnB-dnaB region is presented as an example. Data are also presented on the use of DNA generated by LA PCR for sequencing; they are relevant to LA PCR induced mutations and justify the application of such mapping for sequencing long stretches of bacterial chromosomes.

Regulators of aerobic and anaerobic respiration in Bacillus subtilis

Two Bacillus subtilis genes, designated resD and resE, encode proteins that are similar to those of two-component signal transduction systems and play a regulatory role in respiration. The overlapping resD-resE genes are transcribed during vegetative growth from a very weak promoter directly upstream of resD. They are also part of a larger operon that includes three upstream genes, resABC (formerly orfX14, -15, and -16), the expression of which is strongly induced postexponentially. ResD is required for the expression of the following genes: resA, ctaA (required for heme A synthesis), and the petCBD operon (encoding subunits of the cytochrome bf complex). The resABC genes are essential genes which encode products with similarity to cytochrome c biogenesis proteins. resD null mutations are more deleterious to the cell than those of resE. resD mutant phenotypes, directly related to respiratory function, include streptomycin resistance, lack of production of aa3 or caa3 terminal oxidases, acid accumulation when grown with glucose as a carbon source, and loss of ability to grow anaerobically on a medium containing nitrate. A resD mutation also affected sporulation, carbon source utilization, and Pho regulon regulation. The data presented here support an activation role for ResD, and to a lesser extent ResE, in global regulation of aerobic and anaerobic respiration i B.subtilis.

Identification of six novel autophosphorylation sites on fibroblast growth factor receptor 1 and elucidation of their importance in receptor activation and signal transduction

Fibroblast growth factor receptor (FGFR) activation leads to receptor autophosphorylation and increased tyrosine phosphorylation of several intra cellular proteins. We have previously shown that autophosphorylated tyrosine 766 in FGFR1 serves as a binding site for one of the SH2 domains of phospholipase Cy and couples FGFR1 to phosphatidylinositol hydrolysis in several cell types. In this report, we describe the identification of six additional autophosphorylation sites (Y-463, Y-583, Y-585, Y-653, Y-654 and Y-730) on FGFR1. We demonstrate that autophosphorylation on tyrosines 653 and 654 is important for activation of tyrosine kinase activity of FGFR1 and is therefore essential for FGFR1-mediated biological responses. In contrast, autophosphorylation of the remaining four tyrosines is dispensable for FGFR1-mediated mitogen-activated protein kinase activation and mitogenic signaling in L-6 cells as well as neuronal differentiation of PC12 cells. Interestingly, both the wild-type and a mutant FGFR1 (FGFR1-4F) are able to phosphorylate Shc and an unidentified Grb2-associated phosphoprotein of 90 kDa (pp90). Binding of the Grb2/Sos complex to phosphorylated Shc and pp90 may therefore be the key link between FGFR1 and the Ras signaling pathway, mito-genesis, and neuronal differentiation.

Induction of mitogen-activated protein kinase phosphatase 1 by the stress-activated protein kinase signaling pathway but not by extracellular signal-regulated kinase in fibroblasts

The intracellular mechanisms involved in the activation of extracellular signal-regulated kinase (ERK) are relatively well understood. However, the intracellular signaling pathways which regulate the termination of ERK activity remain to be elucidated. Mitogen-activated protein kinase phosphatase 1 (MKP-1) has been shown to dephosphorylate and inactivate ERK in vitro and in vivo. In the present study, we show in NIH3T3 fibroblasts that activation of the stress-activated protein kinase (SAPK) pathway by either specific extracellular stress stimuli or via induction of MEKK, an upstream kinase of SAPK, results in MKP-1 gene expression. In contrast, selective stimulation of the ERK pathway by 12-O-tetradecanoylphorbol-13-acetate or following expression of constitutively active MEK, the upstream dual specificity kinase of ERK did not induce the transcription of MKP-1. Hence, these findings demonstrate the existence of cross-talk between the ERK and SAPK signaling cascades since activation of SAPK induced the expression of MKP-1 that can inactivate ERK. This mechanism may modulate the cellular response to stimuli which employ the SAPK signal transduction pathway.

Differential long-term regulation of MEK and of p42 MAPK in rat glomerular mesangial cells

Constitutive stimulation of the mitogen-activated protein kinase (MAPK) activator MAPK/ERK kinase (MEK) is sufficient to promote long-term events such as cell differentiation, proliferation, and transformation. To evaluate a possible mechanism for the chronic regulation of MEK and p42 MAPK, we studied the long-term effects of fetal bovine serum (FBS), the G protein-coupled receptor agonist endothelin-1 (ET-1), and the protein tyrosine kinase-coupled receptor agonist platelet-derived growth factor BB (PDGF BB) on MEK and p42 MAPK in glomerular mesangial cells (GMC). FBS, ET-1, and PDGF BB led to a time-dependent increase in MEK-1 mRNA and protein expression without altering p42 MAPK mRNA and protein levels. FBS also induced MEK-1 mRNA expression in diverse cell types, including NIH/3T3 fibroblasts, A7r5 vascular smooth muscle cells, and Chinese hamster ovary cells. In GMC, cycloheximide inhibited MEK-1 mRNA induction but stimulated p42 MAPK mRNA expression in the absence and presence of FBS, ET-1, or PDGF. The FBS-induced increase in MEK-1 mRNA was accompanied by a sustained enhancement of MEK activity, as assessed by the ability of immunoprecipitated p45 MEK to activate recombinant p42 MAPK and hence phosphorylate myelin basic protein, and p42 MAPK activity. We conclude that, in GMC, MEK-1 acts like a delayed-early gene and that it can be chronically induced at the mRNA and protein level.

Activation of the EGF receptor by insertional mutations in its juxtamembrane regions

Ligand dependent activation of receptor tyrosine kinases is mediated by an allosteric dimerization process that is responsible for the stimulation of protein tyrosine kinase activity and receptor autophosphorylation. In order to gain further insight into the processes which control this process, we have generated EGF receptor mutants that contain inserts of 20-40 amino acids in their juxtamembrane regions, on each side of the receptor's single transmembrane domain. An EGF receptor mutant with an insertion on the cytoplasmic side of the transmembrane domain exhibited typical EGF binding characteristics, ligand-dependent tyrosine autophosphorylation, as well as ligand-induced DNA synthesis. However, an EGF receptor mutant with an insertion on both sides of the transmembrane domain was found to be constitutively activated. This mutant also exhibited dramatically reduced EGF binding, but dimerized and had enhanced tyrosine kinase activity even in the absence of ligand. Moreover, NIH3T3 cells expressing this mutant receptor formed colonies in soft agar in the absence of EGF. This represents a novel example of a constitutively activated receptor, and provides further support for receptor dimerization as a mechanism for activation of EGFR and other receptor tyrosine kinases.

Cloning and characterization of the Bacillus subtilis birA gene encoding a repressor of the biotin operon

The Bacillus subtilis birA gene, which regulates biotin biosynthesis, has been cloned and characterized. The birA gene maps at 202 degrees on the B. subtilis chromosome and encodes a 36,200-Da protein that is 27% identical to Escherichia coli BirA protein. Three independent mutations in birA that lead to deregulation of biotin synthesis alter single amino acids in the amino-terminal end of the protein. The amino-terminal region that is affected by these three birA mutations shows sequence similarity to the helix-turn-helix DNA binding motif previously identified in E. coli BirA protein. B. subtilis BirA protein also possesses biotin-protein ligase activity, as judged by its ability to complement a conditional lethal birA mutant of E. coli.

Nucleotide sequence of the Bacillus subtilis dnaD gene

The dnaD gene of Bacillus subtilis was identified within a 104 kb DNA segment cloned into a yeast artificial chromosome. The nucleotide sequence of the wild type and dnaD23 mutant genes were determined. dnaD is predicted to encode a protein of 232 amino acids with no similarity to proteins in the data banks.

The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products

A gene was found in Bacillus subtilis which encodes a protein highly homologous to the Escherichia coli rpsA gene product, the S1 ribosomal protein. The B. subtilis protein contains the domain responsible for binding to ribosomes and two S1 motifs, instead of four as found in the E. coli protein. The B. subtilis protein is similar in this way to the equivalent protein of plant chloroplast ribosomes, supposed to be the counterpart of E. coli S1. The gene is expressed during vegetative growth in B. subtilis at the transcriptional and translational levels, as judged by Northern hybridization and expression in a translational fusion with a reporter gene. In contrast to the E. coli situation, it can be inactivated without dramatic effects on cell viability. Southern hybridization of the B. subtilis DNA fragment encoding this gene revealed specific homologous fragments in all other Gram-positive bacteria tested. The hybridization pattern with B. stearothermophilus suggests the presence of at least two homologous genes in this bacterium. We show that in B. subtilis the ORF preceding the rpsA homologue encodes a protein which is highly similar to the product of the E. coli mssA gene which is located upstream of rpsA. Again, in contrast to the E. coli situation, where these genes are co-transcribed, in B. subtilis they are separated by a transcription terminator and the mssA homologue is transcribed during sporulation. We suggest that during the evolution very similar structures and genetic organization of these two genes were conserved but acquired different functions in Gram-negative and Gram-positive bacteria.

Polymerase chain reaction mediated localization of RFLP clones to microisolated translocation chromosomes of barley

A new strategy has been devised and used for the physical localization of genetically mapped restriction fragment length polymorphism (RFLP) clones to barley chromosomes. Morphologically distinct translocation chromosomes from synchronized root-tip meristems were microisolated and their DNA was used as a template for polymerase chain reaction with sequence-specific primers. Four RFLP clones were assigned to cytologically defined segments of chromosome 5. This related approximately one-third of the map length of linkage group 5 to approximately one-fifth of the mitotic metaphase length of chromosome 5. The technique may substantially contribute to the connection of the RFLP-based genetic linkage maps with cytological markers of the barley chromosomes.

Internalization of fibroblast growth factor receptor is inhibited by a point mutation at tyrosine 766

Binding of fibroblast growth factor (FGF) to the fibroblast growth factor receptor leads to autophosphorylation of the receptor on several tyrosine residues. Wild-type FGF receptor 1 (flg) and a mutated receptor (Y766F), in which an autophosphorylation site (Tyr-766) was mutated to phenylalanine, were expressed in rat myoblasts and in hematopoietic Ba/F3 cells. It was found that the point mutation at Tyr-766 resulted in a decrease in FGF receptor internalization, as well as a reduction in both ligand-induced FGF receptor down-regulation and degradation. It has been shown previously that phosphorylation of Tyr-766 is essential for interaction with phospholipase C gamma and that the Y766F FGF receptor mutant is unable to stimulate phosphatidylinositol hydrolysis and Ca2+ release from internal stores. The results presented in this report indicate that Tyr-766 is also essential for cellular trafficking of FGF receptor.

Stabilization of an active dimeric form of the epidermal growth factor receptor by introduction of an inter-receptor disulfide bond

Populations of the epidermal growth factor receptor (EGFR) with both high and low affinity for EGF are found on the surface of cells. It has been hypothesized that the high-affinity state of the EGFR represents the receptor dimer and that this is also the kinase-active form. We describe here studies aimed at addressing this question directly. To stabilize homodimers of EGFR, we have generated a mutated form of the receptor by inserting a cysteine residue in the extracellular juxtamembranous region, in order to cross-link the extracellular domains of two receptors via disulfide bond formation. The mutation resulted in ligand-induced appearance of covalently linked EGF receptor dimers and, in parallel, increased the number of high-affinity receptors present on the surface of cells expressing the mutated EGFR. Comparison of the tyrosine kinase activity of the covalently linked dimeric and the monomeric forms of the EGF receptor, separated by sucrose density gradient centrifugation, showed that the dimer was significantly more active than monomer in the phosphorylation of exogenous substrate. We conclude that the dimeric form of the EGF-receptor represents the active form, and that dimer formation is associated with the appearance of high-affinity binding EGF receptors on the cell surface.

The transcriptional organization of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci

The genetic organization of the spoVAF-serA area of the Bacillus subtilis chromosome and its putative transcription map have been derived from analysis of the nucleotide sequence. In order to confirm this transcription map as regards size of transcripts and to determine growth conditions for their appearance, we undertook Northern hybridization analysis of total RNA from vegetatively growing and sporulating cells. Twenty-three distinct transcripts were thus identified, 14 of which were predicted from sequence analysis and nine of which were not predicted. Eight of the latter are homologous to open reading frames identified by sequence analysis but were not expected, since no obvious promoter or terminator was found in the sequence. The last unexpected transcript does not correspond to an ORF and might identify a novel gene. Three predicted transcripts were not detected. The transcripts were classified in four groups as (i) constitutive, (ii) regulated by nutritional depletion, (iii) specific for sporulation, and (iv) possibly regulated temporally. These studies demonstrate that systematic Northern analysis of a bacterial chromosome region is a useful complement to sequence analysis.

The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data

Three different lambda phage clones with overlapping inserts of Bacillus subtilis DNA, which cover the region from spoIIAA to serA, have been isolated. The nucleotide sequence of their inserts, starting after spoVAF and ending at serA, has been determined. A contiguous sequence of 35,354 bp was established, including previously analysed overlapping adjacent regions. Within the newly determined sequence 31 open reading frames (ORFs) with putative ribosome-binding sites have been found. Nine of them correspond to previously sequenced and characterized genes: spo-VAF, lysA, sipS, ribG, ribB, ribA, ribH, ribTD and dacB. Comparison of the amino acid sequences of the products encoded by the other ORFs to known proteins allowed putative functions to be assigned to seven of these ORFs. Among these are the following: (i) the ppiB gene, encoding a cytoplasmic peptidylprolyl isomerase; (ii) two pairs of signal-transducers, one homologous to phoR-phoP of B. subtilis, encoding regulators of phosphatase biosynthesis, and the second to the fecI-fecR of Escherichia coli, which is responsible for the regulation of the citrate-dependent iron (III) transport system; (iii) aroC and serA genes, involved in the biosynthesis of aromatic amino acids and serine, respectively, the function of which has been confirmed by constructing corresponding mutants with disrupted ORFs. The organization of putative operons has been postulated on the basis of the sequences of their transcription terminators, promoters and regulatory elements.

Aggregation-induced activation of the epidermal growth factor receptor protein tyrosine kinase

Various agents are able to stimulate the EGF receptor protein tyrosine kinase in the absence of ligand binding. To characterize their mechanism of action, we investigated their effects on the kinase activity of the intracellular domain of the EGF receptor (EGFR-IC). EGFR-IC (67 kDa) lacking the extracellular domain and transmembrane segment of the EGF receptor, but retaining kinase and autophosphorylation domains, was produced and purified as a soluble, cytoplasmic protein from Sf9 insect cells infected with a recombinant baculovirus. EGFR-IC was able to undergo autophosphorylation in a manner similar to full-length EGFR. Synthetic substrate peptides showed similar affinity to EGFR-IC as to the full-length receptor. The activity of the EGFR-IC was found to be dependent on divalent cations, Mn2+ being a more potent activator than Mg2+. Agents capable of aggregating the kinase by direct interaction (cross-linking antibodies, polycations) or through altering the surrounding solvent structure and thereby decreasing protein solubility [ammonium sulfate, poly(ethylene glycol), 2-methyl-2,4-pentanediol] activated the kinase in a manner which correlated with their ability to precipitate the EGFR intracellular domain. The widely different chemical nature of these agents suggests that they do not act by direct interaction with specific allosteric regulatory sites, but rather by facilitating the interactions between kinase molecules. These results support the hypothesis that full-length receptor aggregation itself, induced by ligand binding to the extracellular domain, results in intracellular domain interactions and the activation of kinase activity.

Characterization of the platelet-derived growth factor beta-receptor kinase activity by use of synthetic peptides

Synthetic peptides derived from the sequence surrounding tyrosine-857 in the human platelet-derived growth factor (PDGF) beta-receptor were used to elucidate the requirement for length and presence of negative and positively charged amino acids in substrates of the PDGF beta-receptor protein tyrosine kinase. The measured Km for the different peptides were all in the range 1-10 mM. A peptide of only five amino acids, lacking acidic amino acid residues, were found to be substrates for the receptor kinase. Ligand binding was found to stimulate the phosphorylation of peptides mainly by lowering the Km both for peptide and for ATP. Only minor changes in the Vmax occurred upon stimulation with PDGF. The reaction mechanism was found to be sequential, i.e. both the peptide and ATP have to bind to the enzyme before any product is released.

Recycling of epidermal growth factor-receptor complexes in A431 cells

The fate of epidermal growth factor (EGF) after internalization by human carcinoma A431 cells has been studied. Cells were allowed to internalize 125I-EGF for 10 min at 37 degrees C and treated with acid/salt solution to remove non-internalized ligand. Further incubation of these '125I-EGF-loaded' cells at 37 degrees C results in rapid recycling of internalized 125I-EGF-receptor complexes back to the cell surface. Recycling was assessed by measuring the increase in plasma membrane pool of 125I-EGF-receptor complexes as they became sensitive to acid/salt treatment, cross-linking with the membrane impermeant reagent bis(sulfosuccinimidyl)suberate and competitive substitution by unlabeled EGF. Moreover, redistribution of 125I-EGF-receptor complexes from endosomes to the plasma membrane was demonstrated using a subcellular fractionation technique. More than 50% of the total internalized EGF was found to be capable of recycling. The rate of recycling was significantly higher than that of EGF degradation in lysosomes. It was shown that EGF/receptor recycling is an energy-requiring and temperature-dependent process. Fluorescence microscopy studies demonstrate that endosomes located in a region adjacent to the Golgi complex are involved in the the recycling of EGF-receptor complexes in A431 cells. The data obtained suggest that dissociation of EGF from internalized receptor is not necessary for EGF receptor recycling.