bluuebunny/crossref_metadata_2025_split huggingface dataset:
NoIR controls expression of the Rhizobium meliloti nodulation genes involved in the core Nod factor synthesis
Authors: Cren Michèle , Kondorosi Adam , Kondorosi Eva 
Published: October 2006

SummaryThe synthesis of Rhizobium meliloti Nod signal molecules, encoded by the nod gene products, is finely regulated. A negative control of plasmid‐borne nod gene expression is provided by the NoIR repressor encoded by the chromosomal noIR gene. NoIR was previously shown to downregulate the expression of the activator nodD1 gene and the common nodABC operon by binding to an overlapping region of the two promoters adjacent to the n1 nod‐box (Kondorosi et al., 1989). We demonstrate here that NoIR also controls the expression of two additional genes, nodD2 and nodM, but does not directly regulate the expression of the host‐specific nod genes located downstream of the n2, n3 and n5 nod‐boxes. Thus, the nod genes are differentially regulated by NoIR and only those providing common nodulation functions, by determining the synthesis of the core Nod factor structure, are subjected to this negative regulation. Furthermore, NoIR has a strong negative effect on the production of Nod metabolites, the level of which may serve as a fine‐tuning mechanism for optimal nodulation, specific to host‐plant genotypes. In addition, it elicits preferential synthesis of Nod factors carrying unsaturated C16 fatty acids. Expression of noIR was high both in the free‐living bacterium and in the bacteroid and it was downregulated by its own product and by the nod gene inducer luteolin.
A 40 kb chromosomal fragment encoding Salmonella typhimurium invasion genes is absent from the corresponding region of the Escherichia coli K‐12 chromosome
Authors: Mills Debra M. , Bajaj Vivek , Lee Catherine A. 
Published: October 2006

SummaryMany Salmonella typhimurium genes are required for bacterial entry into host cells. P22 transduction analysis has localized several invasion loci near minute 59 on the S. typhimurium chromosome. To further characterize the 59–60 min chromosomal region, we determined the physical and genetic map of 85 kb of S. typhimurium DNA between srl and cysC. It was previously shown that some of the invasion genes from this region are not present in Escherichia coli K‐12. We examined whether other S. typhimurium genes on the 85 kb of DNA were similarly absent from E. coli We found that a contiguous 40 kb fragment of the S. typhimurium chromosome which encodes invasion genes is absent from the corresponding region of the E. coli K‐12 chromosome and may represent a pathogenicity island. We speculate that acquisition of the 40 kb region must have significantly advanced the evolution of Salmonella as a pathogen.
Topological analyses of the l‐fucose‐H+ symport protein, FucP, from Escherichia coli
Authors: Gunn Frank J. , Tate Christopher G. , Sansom Clare E. , Henderson Peter J. F. 
Published: October 2006

SummaryThe transport of l‐fucose into Escherichia coli is mediated by the l‐fucose‐H+ symport protein (FucP). The fucP gene has been sequenced and encodes a hydrophobic protein that contains 438 amino acid residues, with a predicted Mr of 47773. The hydropathic profile of FucP indicates 10 to 12 hydrophobic regions that could span the membrane as α‐helices. A 12‐helix model with the N‐ and C‐termini located in the cytoplasm was derived from the hydropathic profile and from application of the ‘positive inside’ rule. This model was tested using β‐lactamase fusion technology. Analyses of 62 different FucP‐β‐lactamase fusions suggested that the FucP protein crosses the cytoplasmic membrane of E. coli 12 times, with the N‐ and C‐termini in the cytoplasm. From measurements of [14C]‐l‐fucose uptake, it was deduced that the last putative transmembrane region must be complete for transport activity to be retained and that the four C‐terminal residues were unnecessary for transport activity. Fourier transform analyses show that all the predicted helices contain a periodicity that enables hydrophobic/hydrophilic faces to be identified; these were particularly evident in putative helices 1, 3, 4, 5, 6, 10 and 11.
The regulation of transcription initiation by integration host factor
Authors: Goosen Nora , van de Putte Pieter 
Published: October 2006

SummaryIntegration host factor (IHF) of Escherichia coli is an asymmetric histone‐like protein that binds and bends the DNA at specific sequences. IHF functions as an accessory factor in a wide variety of processes including replication, site‐specific recombination and transcription. In many of these processes IHF was shown to act as an architectural element which helps the formation of nucleo‐protein complexes by bending of the DNA at specific sites. This MicroReview shows how such a structural role of IHF can influence the initiation of transcription. In addition, it summarizes the evidence indicating that IHF can stimulate transcription via a direct interaction with RNA polymerase and explores the possibility that the asymmetry of the IHF protein might reflect such an interaction
Mutational analysis of the ganglioside‐binding activity of the type II Escherichia coli heat‐labile enterotoxin LT‐IIb
Authors: Connell Terry D. , Holmes Randall K. 
Published: October 2006

SummaryThe Escherichia coli type II heat‐labile enterotoxin LT‐IIb consists of a single A polypeptide and five B polypeptides. The A polypeptide is responsible for the toxic activity, and the B polypeptides function to bind the toxin to gangliosides on the surface of the plasma membrane. Previous studies on the related type II enterotoxin LT‐IIa demonstrated the importance of threonine (Thr) residues at positions 13, 14, and 34 in the mature B polypeptide for ganglioside GD1b‐binding activity. In this study, we used site‐specific mutagenesis to investigate ganglioside GD1a‐binding activity of the B polypeptide of LT‐IIb. We determined that Thr‐13 and Thr‐14 were involved in binding of ganglioside GD1 a by the B polypeptides of LT‐IIb but that Thr‐34 was not essential. Substitution of serine, but not other amino acids, at position 13 or 14 in the B polypeptide of LT‐IIb resulted in retention of ganglioside‐binding activity equivalent to that of the wild‐type enterotoxin, providing strong evidence that the hydroxyl groups of threonine or serine at positions 13 and 14 are important for the ganglioside‐binding activity of LT‐IIb. Chimeric genes that expressed hybrids of the B polypeptides of LT‐IIb and LT‐IIa were also constructed, and analysis of the hybrids showed that the specificity of their ganglioside‐binding activity was determined by the N‐terminal half of the molecule.
Genes acrA and acrB encode a stress‐induced efflux system of Escherichia coli
Authors: Ma Dzwokai , Cook David N. , Alberti Marie , Pon Ning G. , Nikaido Hiroshi , Hearst John E. 
Published: October 2006

SummaryDefined mutations of acrA or acrB (formerly acrE) genes increased the susceptibility of Escherichia coli to a range of small inhibitor molecules. Deletion of acrAB increased susceptibility to cephalothin and cephaloridine, but the permeability of these β‐lactams across the outer membrane was not increased. This finding is inconsistent with the earlier hypothesis that acrAB mutations increase drug susceptibility by increasing the permeability of the outer membrane, and supports our model that acrAB codes for a multi‐drug efflux pump. The natural environment of an enteric bacterium such as E. coli is enriched in bile salts and fatty acids. An acrAB deletion mutant was found to be hypersusceptible to bile salts and to decanoate. In addition, acrAB expression was elevated by growth in 5mM decanoate. These results suggest that one major physiological function of AcrAB is to protect E. coli against these and other hydrophobic inhibitors. Transcription of acrAB is increased by other stress conditions including 4% ethanol, 0.5 M NaCl, and stationary phase in Luria‐Bertani medium. Finally, acrAB expression was shown to be increased in mar (multiple‐antibiotic‐resistant) mutants.
Characterization and distribution of two insertion sequences, IS1191 and iso‐IS981, in Streptococcus thermophilus: does intergeneric transfer of insertion sequences occur in lactic acid bacteria co‐cultures?
Authors: Guédon G. , Bourgoin F. , Pébay M. , Roussel Y. , Colmin C. , Simonet J. M. , Decaris B. 
Published: October 2006

SummaryA chromosomal repeated sequence from Streptococcus thermophilus was identified as a new insertion sequence (IS), IS1191. This is the first IS element characterized in this species. This 1313 bp element has 28 bp imperfect terminal inverted repeats and is flanked by short direct repeats of 8bp. The single large open reading frame of IS1191 encodes a 391‐amino‐acid protein which displays homologies with transposases encoded by IS1201 from Lactobacillus helveticus (44.5% amino‐acid sequence identity) and by the other ISs of the IS256 family. One of the copies of IS 1191 is inserted into a truncated iso‐IS981 element. The nucleotide sequences of two truncated iso‐IS981 s from S. thermophilus and the sequence of IS981 element from Lactococcus lactis share more than 99% identity. The distribution of these insertion sequences in L. lactis and S. thermophilus strains suggests that intergeneric transfers occur during co‐cultures used in the manufacture of cheese.
Overexpression of wild‐type and mutant NDP kinase in Dictyostelium discoideum
Authors: Sellam Olivier , Véron Michel , Hildebrandt Martin 
Published: October 2006

SummaryNucleoside diphosphate (NDP) kinase has a central role in the synthesis of (deoxy‐)trinucleotides. In addition, mutations in the gene encoding NDP kinase have been shown to have important consequences for Drosophila development and mammalian tumorogenesis. We have overexpressed, in Dictyostelium discoideum, a genomic clone encoding the enzyme NDP kinase. The concomitant increase in the levels of RNA and enzyme activity identifies a 5′ non‐coding genomic region of 0.9 kb as being the complete promoter region. Overexpression of wild‐type NDP kinase has no effect on development. This is also true for an inactive mutant H122C that does not have a dominant inhibitor effect. Overexpression of the P105G mutant NDP kinase, which is known to be affected in its stability in vitro, only leads to a small increase in total NDP‐kinase activity. Thermal and chemical denaturation experiments demonstrate the formation of hexameric hybrids between wild‐type and mutant monomers.
Protein exporter function and in vitro ATPase activity are correlated in ABC‐domain mutants of HlyB
Authors: Koronakis Eva , Hughes Colin , Milisav Irina , Koronakis Vassilis 
Published: October 2006

SummaryThe Escherichia coli toxin exporter HlyB comprises an integral membrane domain fused to a cytoplasmic domain of the ATP‐binding casette (ABC) super‐family, and it directs translocation of the 110kDa haemolysin protein out of the bacterial cell without using an N‐terminal secretion signal peptide. We have exploited the ability to purify the soluble HlyB ABC domain as a fusion with glutathione S‐transferase to obtain a direct correlation of the in vivo export of protein by HlyB with the degree of ATP binding and hydrolysis measured in vitro. Mutations in residues that are invariant or highly conserved in the ATP‐binding fold and glycine‐rich linker peptide of prokaryotic and eukaryotic ABC transporters caused a complete less of both HlyB exporter function and ATPase activity in proteins still able to bind ATP effectively and undergo ATP‐induced conformational change. Mutation of less‐conserved residues caused reduced export and ATP hydrolysis, but not ATP binding, whereas substitutions of poorly conserved residues did not impair activity either in vivo or in vitro. The data show that protein export by HlyB has an absolute requirement for the hydrolysis of ATP bound by its cytoplasmic domain and indicate that comparable mutations that disable other prokaryotic and eukaryotic ABC transporters also cause a specific loss of enzymatic activity.
Differential expression of mal genes under cAMP and endogenous inducer control in nutrient‐stressed Escherichia coli
Authors: Notley Lucinda , Ferenci Thomas 
Published: October 2006

SummaryLamB glycoporin has an important general role in carbohydrate uptake during growth at low extracellular sugar concentrations. lamB and mal regulon induction during glucose starvation and glucose‐limited continuous culture was investigated using lacZ fusions. A low‐level burst of lamB induction occurred upon entry into glucose starvation‐induced stationary phase but returned to basal levels during continued nutrient deprivation. Glucose‐limited continuous culture elicited much higher expression of transporter genes in the mal regulon, as well as [14C]‐maltose‐transport activity; malEFG and malKlamB operons in glucose‐limited chemostats were expressed to close to half of the level of maltose‐induced batch cultures. Limitation‐induced expression was dependent on both Crp‐cAMP and MalT activation but was independent of RpoS function. As expected for a gene with a Crp‐controlled promoter, malT expression was maximal under conditions which elicited the highest cAMP levels, but lamB induction did not behave in a corresponding fashion. Rather, maximal lamB induction occurred at rapid but suboptimal growth rates with micromolar or submicromolar medium glucose. Maximal transport and lamB induction coincided with increased endogenous maltotriose (inducer) concentrations during growth on glucose. Hence regulation of glycoporin and the maltose‐transport system is not a starvation‐ or stationary‐phase response but facilitates the adaptation of Escherichia coli to low‐nutrient environments through endoinduction.
Control of lytic development in the Streptomyces temperate phage φC31
Authors: Wilson Stuart E. , Ingham Colin J. , Hunter Iain S. , Smith Margaret C. M. 
Published: October 2006

SummaryThe repressor gene. c, is required for maintenance of lysogeny in the Streptomyces phage φC31. The c gene expresses three in‐frame N‐terminally different protein isoforms at least one of which is thought to bind to a 17bp highly conserved inverted repeat (CIR) sequence found at 18 (or more) loci throughout the φC31 genome. Here we present evidence that one of these loci, CIR6, and its interaction with the products of the repressor gene are critical in the control of the lytic pathway in φC31. To the right of CIR6, according to the standard map of φC31, an ‘immediate‐early’ promoter. ap1, was discovered after insertion of a fragment containing CIR6 upstream of a promoterless kanamycin‐resistance gene. aphll, to form pCIA2. pCIA2 conferred kanamycin resistance upon Streptomyces coelicolor A3(2) but not upon a φC31 lysogen of S. coelicolor. Operator‐constitutive (Oc) mutants of pCIA2 were isolated and the mutations lay in CIR6, i.e. CIR6:G14T and CIR6:C2A. Primer extension analysis of RNA prepared from an induced, temperature‐sensitive lysogen of S. coelicolor localized a mRNA 5′ endpoint 21 bp to the right of CIR6. The importance of the ap1/CIR6 region in the regulation of lytic growth was demonstrated by the analysis of a virulent mutant, φC31 vir1, capable of forming plaques on an S. coelicolorφC31 lysogen, φC31 vir1 contained a DNA inversion with the breakpoints lying within the integrase gene (which lies approximately 7kbp to the right of CIR6) and in the essential early region between CIR6 and the ‐10 sequence for ap1. The separation of ap1 from its operator was thought to be the basis for the virulent phenotype in φC31 vir1. Band‐shift assays and DNase I footprinting experiments using purified 42kDa repressor isoform confirmed that CIRs 5 and 6 were indeed the targets for binding of this protein. The 42 kDa repressor bound to CIR6 with higher affinity than to CIR5 in spite of their identical core sequences. Repressor bound at CIR6 facilitated binding at CIR5. The high‐affinity binding to CIR6 was abolished with the Oc mutant, CIR6:G14T. Hydroxyl radical footprinting and dimethyl sulphate methylation protection of the 42 kDa repressor–CIR6 interaction suggested that the protein bound in the major groove and to one face of the DNA.
Identification of novel HXT genes in Saccharomyces cerevisiae reveals the impact of individual hexose transporters on qlycolytic flux
Authors: Reifenberger E. , Freidel K. , Ciriacy M. 
Published: October 2006

SummaryIn Saccharomyces cerevisiae, hexose uptake is mediated by HXT proteins which belong to a superfamily of monosaccharide facilitators. We have identified three more genes that encode hexose transporters (HXT5, 6, 7). Genes HXT6 and HXT7 are almost identical and located in tandem 3′ adjacent to HXT3 on chromosome IV. We have constructed a set of congenic strains expressing none or any one of the seven known HXT genes and followed growth and flux rates for glucose utilization. The hxt null strain does not grow on glucose, fructose or mannose, and both glucose uptake and flux rate were below the detection level. Expression of either HXT1, 2, 3, 4, 6 or 7 is basically sufficient for aerobic growth on these sugars. In most of the constructs, glucose was the preferred substrate compared to fructose or mannose. There is a considerable variation in flux and growth rates with 1% glucose, dependent on the expression of the individual HXT genes. Expression of either HXT2, 6 or 7 in the null background is sufficient for growth on 0.1% glucose, while growth of strains with only HXT1, 3 or 4 requires higher (≥1%) glucose concentrations. These results demonstrate that individual HXT proteins can function independently as hexose transporters, and that most of the metabolically relevant HXT transporters from S. cerevisiae have been identified.
Collapse and repair of replication forks in Escherichia coli
Authors: Kuzminov Andrei 
Published: October 2006

SummarySingle‐strand interruptions in a template DNA are likely to cause collapse of replication forks. We propose a model for the repair of collapsed replication forks in Escherichia coli by the RecBCD recombinational pathway. The model gives reasons for the preferential orientation of Chi sites in the E. coli chromosome and accounts for the hyper‐rec phenotype of the strains with increased numbers of single‐strand interruptions in their DNA. On the basis of the model we offer schemes for various repeat‐mediated recombinational events and discuss a mechanism for quasi‐conservative DNA replication explaining the recombinational repair‐associated mutagenesis.
The role of the YAP1 and YAP2 genes in the regulation of the adaptive oxidative stress responses of Saccharomyces cerevisiae
Authors: Stephen Duncan W. S. , Rivers Stuart L. , Jamieson Derek J. 
Published: October 2006

SummaryThe YAP1 and YAP2 genes encode yeast transcription factors of the c‐jun family. We show that yeast mutants deleted for either the YAP1 or the YAP2 genes are hypersensitive to oxidants, particularly H2O2, and that these genes play a role in regulating the induction of the H2O2 adaptive stress response in Saccharomyces cerevisiae. They do not significantly affect the regulation of the superoxide adaptive stress response. The intrinsic resistance of stationary‐phase and respiring yeast cells towards superoxide anions is unaffected by deletion of the YAP1 and YAP2 genes. However, resistance towards H2O2 under these conditions is significantly reduced. We show that expression of the yeast GSH1 gene (encoding γ‐glutamylcysteine synthetase) and the SSA1 gene (encoding an HSP70 isoform) are induced by oxidants. Unlike the SSA1 and thioredoxin (TRX2) genes, expression of the GSH1 gene is more strongly induced by superoxide anions than by H2O2. In the absence of added oxidants, transcription of the GSH1 gene is reduced in strains carrying the yap1 deletion. However, we show that Yap1 is not required for the superoxide anion‐mediated induction of GSH1 gene expression. Furthermore, while the H2O2‐mediated induction of SSA1 expression is shown to be YAP1 dependent, the heat‐shock‐mediated induction of the SSA1 gene does not require YAP1. We also present evidence to show that the YAP2 gene does not regulate the expression of the TRX2, SSA1 or GSH1 genes.
Molecular cloning and functional expression of bacteriophage PK1E‐encoded endoneuraminidase Endo NE
Authors: Gerardy‐Schahn Rita , Bethe Andrea , Brennecke Thomas , Mühlenhoff Martina , Eckhardt Matthias , Ziesing Stefan , Lottspeich Friedrich , Frosch Matthias 
Published: October 2006

SummaryHomopolymeric α‐2,8‐linked sialic acid (PSA) has been found as a capsular component of sepsis‐ and meningitis‐causing bacterial pathogens, and on eukaryotic cells as a post‐translational modification of the neural cell adhesion molecule (NCAM). The polysaccharide is specifically recognized and degraded by a phage‐encoded enzyme, the endo‐N‐acetylneuraminidase E (Endo NE). Endo NE therefore has become a valuable tool in the study of bacterial pathogenesis and eukaryotic morphogenesis. In this report we describe the molecular cloning of Endo NE and the expression of a functionally active recombinant enzyme. The cloned DNA sequence (2436 bp) encodes a polypeptide of 811 amino acids, which at the 5′ end contains a totally conserved neuraminidase motif. Expressed in Escherichia coli, the enzyme migrates as a single band of approximately 74 kDa in SDS‐PAGE. A central domain of 669 amino acid residues is about 90% homologous to the recently cloned Endo NF. Both phage‐induced lysis of bacteria and the catalysis of PSA degradation by the recombinant enzyme are efficiently inhibited by a polyclonal antiserum raised against the intact phage particle. The C‐terminal region seems to be essential to enzymatic functions, as truncation of 32 amino acids outside the homology domain completely abolishes Endo NE activity. Our data also indicate that the 38 kDa protein, previously assumed to be a subunit of the Endo NE holoenzyme, is the product of a separate gene locus and is not necessary for in vitro depolymerase activity.
Identification and characterization of pilG, a highly conserved pilus‐assembly gene in pathogenic Neisseria
Authors: Tønjum Tone , Freitag Nancy E. , Namork Ellen , Koomey Michael 
Published: October 2006

SummaryExpression of type IV pili appears to be a requisite determinant of infectivity for the strict human pathogens Neisseria gonorrhoeae and Neisseria meningitidis. The assembly of these colonization factors is a complex process. This report describes a new pilus‐assembly gene, pilG, that immediately precedes the gonococcal (Gc) pilD gene encoding the pre‐pilin leader peptidase. The nucleotide sequence of this region revealed a single complete open reading frame whose derived polypeptide displayed significant identities to the pilus‐assembty protein PilC of Pseudomonas aeruginosa and other polytopic integral cytoplasmic membrane constituents involved in protein export and competence. A unique polypeptide of Mr 38kDa corresponding to the gene product was identified. A highly related gene and flanking sequences were cloned from a group E polysaccharide‐producing strain of N. meningitidis (Mc). The results indicate that the pilG genes and genetic organization at these loci in Gc and Me are extremely conserved. Hybridization studies strongly suggest that pilG‐related genes exist in commensal Neisseria species and other species known to express type IV pili. Defined genetic lesions were created by using insertional and transposon mutagenesis and moved into the Gc and Me chromosomes by allelic replacement. Chromosomal pilG insertion mutants were devoid of pili and displayed dramatically reduced competence for transformation. These findings could not be ascribed to pilin‐gene alterations or to polarity exerted on pilD expression. The results indicated that PilG exerts its own independent role in neisserial pilus biogenesis.