bluuebunny/crossref_metadata_2025_split huggingface dataset:
The O75X adhesin of uropathogenic Escherichia coli is a type IV collagen‐binding protein
Authors: Westerlund B. , Kuusela P. , Risteli J. , Risteli L. , Vartio T. , Rauvala H. , Virkola R. , Korhonen T. K. 
Published: October 2006

SummaryInteraction of the basement‐membrane binding O75X adhesin of uropathogenic Escherichia coli with various extracellular matrix proteins was studied. The adhesin showed strong binding to type IV collagen immobilized on microtitre plates, whereas other collagens, laminin and fibronectin, were only weakly recognized. Similarly, specific binding of [125I]‐labelled type IV collagen to 075X‐positive bacteria was shown. Interaction of the two proteins was also demonstrated by affinity chromatography of the O75X adhesin on immobilized type IV collagen. The adhesin bound strongly to the immobilized N‐terminal 7S domain of type IV collagen, and the binding of [125I]‐labelled type IV collagen to O75X‐positive bacteria was inhibited by the soluble 7S domain. Binding of O75X to type IV collagen and to its 7S domain was specifically inhibited by chloramphenicol but was not affected by periodate or endoglycosidase‐H treatment of the glycoproteins. Our results show that the 7S domain of type IV collagen is the basement membrane receptor for the O75X adhesin and suggest an interaction based on protein‐protein recognition. Inhibition of the interaction by chloramphenicol favours the supposition that a modified tyrosine is involved in the binding site.
Regulation of exotoxin A synthesis in Pseudomonas aeruginosa: characterization of toxA‐lacZ fusions in wild‐type and mutant strains
Authors: Vasil M. L. , Grant C. C. R. , Prince R. W. 
Published: October 2006

SummaryA mobilizable plasmid which carries the promoter for the exotoxin A (ETA) structural gene fused to lacZ was integrated into the chromosome of wild‐type and mutant strains of Pseudomonas aeruginosa at the toxA locus by homologous recombination. β‐galactosidase synthesis in the strains (cointegrates) carrying the tox4‐lacZ fusions was regulated like ETA synthesis is in P. aeruginosa.Two multicopy plasmids carrying a positive regulatory gene designated toxR were constructed which are identical except with respect to the orientation of toxR to the lacZ promoter on the plasmid. These plasmids were then introduced into P. aeruginosa cointegrate strains. When toxR was using its own promoter, synthesis of β‐galactosidase in the cointegrate strains was increased but the pattern of iron regulation was not altered. In contrast, when the lacZ promoter was directing synthesis of the toxR product in the cointegrate strains, iron regulation of β‐galacto‐sidase and ETA synthesis were abolished.
virG of Agrobacterium tumefaciens plasmid pTiC58 encodes a DNA‐binding protein
Authors: Powell B. S. , Rogowsky P. M. , Kado C. I. 
Published: October 2006

SummaryVirulence genes of the Agrobacterium tumefaciens Ti plasmid are positively regulated by the products of virA and virG. To study the DNA‐binding properties of the VirG protein, a translational fusion between virG and the frpEgene of Escherichia coli was constructed, and antiserum was raised against the encoded fusion protein. Using this antiserum, a protein of Mr= 29000, a size similar to that calculated from the virG nucleotide sequence, was detected in an E. coli strain harbouring a virG expression vector. Both the VirG protein and the fusion protein were found, by filter‐binding and gel retardation analyses, to bind DNA nonspecifically. These data support an existing model for the two‐component regulatory systems of bacteria.
Cloning and analysis of the gene for the major outer membrane lipoprotein from Pseudomonas aeruginosa
Authors: Cornelis P. , Bouia A. , Belarbi A. , Guyonvarch A. , Kammerer B. , Hannaert V. , Hubert J. C. 
Published: October 2006

SummaryThe gene for the Pseudomonas aeruginosa outer membrane lipoprotein I was isolated from a genomic library in the phage λ EMBL3 vector and subsequently subcloned in the low copy‐number, wide host‐range plasmid vector, pKT240. The cloned gene was highly expressed, resulting in the production of a low molecular‐weight protein (8kD) that was found to be associated with the outer membrane. Sequence anatysis showed an open reading frame of 83 amino acids with a putative N‐terminal hydrophobic signal peptide of 19 residues immediately followed by the lipoprotein consensus sequence, GLY‐CYS‐SER‐SER (residues 19–22). The predicted amino acid composition of the mature polypeptide and that of the purified lipoprotein I of P. aeruginosa (Mizuno and Kageyama, 1979) were identical. In contrast with other Gram‐negative outer membrane lipoproteins, conformation predictions suggested that the mature protein was a single alpha helix.
Nucleoprotein structures at positively regulated bacterial promoters: homology with replication origins and some hypotheses on the quaternary structure of the activator proteins in these complexes
Authors: Rajbaud O. 
Published: October 2006

SummaryThe quaternary structure of regulatory proteins undoubtedly plays an important role in the initiation of transcription and DNA replication. To date, the best‐characterized regulatory proteins are oligomers in which protomers are bound together by isologous interactions. From the examples presented in this article, it appears that the formation of certain nucleoprotein complexes implicated in transcription initiation might involve heterologous rather than isologous interactions, allowing differentiation between two classes of transcription activators.
The high‐affinity K+‐translocating ATPase complex from Bacillus acidocaldarius consists of three subunits
Authors: Hafer J. , Siebers A. , Bakker E. P. 
Published: October 2006

SummaryCells of the thermoacidophilic bacterium Bacillus acidocaldarius express a high‐affinity K+‐uptake system when grown at low external K+. A vanadate‐sensitive, K+ ‐ and Mg2+ ‐stimulated ATPase was partially purified from membranes of these cells by solubilization with a non‐ionic detergent followed by ion‐exchange chromatography of the extract. Combinations of non‐denaturing and denaturing electrophoretic separation methods revealed that the ATPase complex consisted of three subunits with molecular weights almost identical to those of the KdpA, B and C proteins, which together form the Kdp high‐affinity, K+ ‐translocating ATPase complex of Escherichia coli. The affinity of the partially purified ATPase from B. acidocaldarius for its substrates K+ (Km 2–3 μM) and ATP (Km 80 μM), its stimulation by various divalent cations, and its inhibition by vanadate (Ki 1–2 μM), bafilomycin A1 (Ki, 20 μM), DCCD (Ki 200 μM) or Ca2+ were also similar to those of the E coli enzyme, indicating that the two K+ ‐translocating ATPases have almost identical properties.
Role of cysteine residues and of metal ions in the regulatory functioning of FNR, the transcriptional regulator of anaerobic respiration in Escherichia coli
Authors: Trageser M. , Unden G. 
Published: October 2006

SummaryFNR, the transcriptional regulator of gene expression of anaerobic respiration in Escherichia coli, contains a cluster of cysteine residues at the amino terminus which resembles the metal‐binding domains of metal‐binding proteins. It is possible, therefore, (i) that FNR binds metals with the cysteines as ligands and (ii) that this property is related to the regulatory function of FNR. These questions were investigated, with the following results.Approximately 2.4 of the 4 cysteine residues of FNR can be alkylated with iodoacetate in permeabilized aerobic or anaerobic bacteria without the addition of reducing agents. The time required for half‐maximal labelling of the cysteines was 50 min in anaerobic bacteria and 6 min in aerobic bacteria. The difference in the reactivity was specific for the cysteines of FNR. These cysteine residues were also highly reactive in anaerobically grown bacteria, when the growth medium contained chelating agents such as 1,10‐phe‐nanthroline (15 μM). The effect of the chelating agents was reversed by an excess of divalent metal ions such as Fe(11) or Cu(11) in the medium. The presence of 1,10‐phenanthroline (10 μM) also inhibits the expression of fumarate reductase, an FNR‐dependent enzyme. These results suggest that FNR exists in two different forms which differ in terms of the reactivity of their cysteine residues to iodoacetate. The interconversion of both forms appears to be regulated by the availability of O2and by the binding of metal ions. The two forms of FNR may be involved in the regulation of O2‐dependent gene expression.
A bacterial c‐type cytochrome can be translocated to the periplasm as an apo form; the biosynthesis of cytochrome cd1 (nitrite reductase) from Paracoccus denitrificans
Authors: Page M. D. , Ferguson S. J. 
Published: October 2006

SummaryAn apo form of cytochrome cd1, (nitrite reductase) of Paracoccus denitrificans has been detected immunologically in the periplasm of a mutant that lacks all c‐type cytochromes. A method for the preparation of apo‐nitrite reductase (lacking both c‐ and d‐type haem) from the holoenzyme of wild‐type cells has been developed. The apoprotein synthesized by the mutant is indistinguishable from the chemically prepared apoprotein in respect of: (i) subunit molecular weight; (ii) formation of a homodimer; (iii) properties on anion exchange chromatography. The holoenzyme has similar properties in respect of (i) and (ii) but behaves differently during anion exchange. A suggested mode of assembly of cytochrome cd1, is trans‐location into the periplasm of a precursor polypeptide, maturation by a signal peptidase to give an apoprotein identical to that prepared chemically from the holoenzyme, followed by insertion of c‐type and d‐type haem in an as yet unknown order.
Cloning and characterization of beta‐lactam biosynthetic genes
Authors: Miller J. R. , Ingolia T. D. 
Published: October 2006

SummarySeven genes coding for two different enzymes of the penicillin/cephalosporin biosynthetic pathway have been cloned from fungal and bacterial sources. Using amino acid sequences derived from the purified enzymes, oligonucleotide probes were designed to hybridize to their cognate genes in a genomic library. The high degree of similarity (57%) between enzymes of bacterial and fungal origin suggests a horizontal transfer of a primordial beta‐lactam pathway, probably from a bacterial cell to a fungal cell. Overproduction of the proteins in Escherichia coli has allowed further study of the mechanism of action of these important enzymes.
Identification, molecular cloning and sequence analysis of a gene cluster encoding the Class II fructose 1,6‐bisphosphate aldolase, 3‐phosphoglycerate kinase and a putative second glyceraldehyde 3‐phosphate dehydrogenase of Escherichia coli
Authors: Alefounder P. R. , Perham R. N. 
Published: October 2006

SummaryTo investigate a possible chromosomal clustering of glycolytic enzyme genes, the complete nucleotide sequence of the 8029 bp insert of Escherichia coli DNA in the ColE1 plasmid pLC33‐5 of the Clarke and Carbon collection (Clark and Carbon, 1976) was determined. Genes (pgk, fda) encoding the phosphoglycerate kinase and Class II fructose 1,6‐bisphosphate aldolase, respectively, of E. coli were identified. The phosphoglycerate kinase was found to be highly homologous in primary structure to the same enzyme from eukaryotic organisms. A further large open reading frame, designated gapB, was also identified, which on the basis of sequence homology, appears to encode another glycolytic enzyme, glyceraldehyde 3‐phosphate dehydrogenase. This putative gene differs significantly from that (designated gapA) already identified as coding for this enzyme in E. coli and which maps elsewhere on the chromosome. The products, if any, of several other open reading frames remain to be identified.
The Rhizobium meliloti host range nodQ gene encodes a protein which shares homology with translation elongation and initiation factors.
Authors: Cervantes E. , Sharma S. B. , Maillet F. , Vasse J. , Truchet G. , Rosenberg C. 
Published: October 2006

SummaryThe Rhizobium meliloti nod region lib is involved in host‐range determination: (i)the presence of region lib is necessary for transfer of alfalfa root hair curling ability to Rhizobium legumlnosarum biovar trifolii; (ii) a mutation in region llb extends the R. meliloti infection host range to Vicia sativa nigra; (iii) dominance of R. meliloti nod genes over R. leguminosarum biovar viciae nod genes is abolished by mutations in region llb. The nucleotide sequence of this region has been determined. Genes corresponding to the two open reading frames identified are designated nodP and nodQ. The predicted amino acid sequence of the NodQ protein shows homology with translation initiation and elongation factors. The consensus sequence involved in the GTP‐binding domain is conserved.
Notes The ribonucleoside diphosphate reductase gene (nrdA) of Escherichia coli carries a repetitive extragenic palindromic (REP) sequence in its 3'structural terminus
Authors: Merino E. , Bolivar F. 
Published: October 2006

SummaryA computer search for repeated sequences led us to identify five REP (repetitive extragenic palindromic) sequences in the 3′ ‐terminal region of the Escherichia coli ribonucleoside diphosphate reductase gene (nrdA). These REP sequences are located within a putative duplicated DNA region, the first of them being part of the carboxy‐terminal coding region of the nrdA gene. This is the first report of a REP sequence within a structural gene and also the first example of a REP sequence apparently generated by DNA duplication.
Molecular genetic analysis of FNR‐dependent promoters
Authors: Eiglmeier K. , Honoré N. , Iuchi S. , Lin E. C. C. , Cole S. T. 
Published: October 2006

SummaryIn enteric bacteria, the expression of many genes encoding various anaerobic electron transfer functions is controlled by FNR, the product of the autoregulated fnr gene. FNR is structurally and functionally homologous to CAP, the catabolite gene activator protein, and increased FNR production strongly stimulates transcription of its target genes. By analysis of RNA produced in vivo the promoters of four FNR‐dependent genes were localized and shown to display a common arrangement. A 22bp dyad symmetry was found about 30 nucleotides upstream of the transcriptional startpoints and a similar sequence was shown to overlap the site of transcription initiation in the negatively controlled fnr gene. The consensus sequence for the half site recognized by FNR (AAA‐TTGAT) is only slightly different from that of CAP (AA‐TGTGA). Studies with two mutant frd promoters from Escherichia coli, displaying altered regulation and FNR response, provided additional evidence for recognition of this sequence by FNR.
Assembly of colicin genes from a few DNA fragments. Nucleotide sequence of colicin D
Authors: Roos U. , Harkness R. E. , Braun V. 
Published: October 2006

SummaryThe nucleotide sequence of a 2.4 kb Dral‐EcoRV fragment of pColD‐CA23 DNA was determined. The segment of DNA contained the colicin D structural gene (cda) and the colicin D immunity gene (cdi). From the nucleotide sequence it was deduced that colicin D had a molecular weight of 74683D and that the immunity protein had a molecular weight of 10057D. The amino‐terminal portion of colicin D was found to be 96% homologous with the same region of colicin B. Both colicins share the same cell‐surface receptor, FepA, and require the TonB protein for uptake. A putative TonB box pentapeptide sequence was identified in the amino terminus of the colicin D protein sequence. Since colicin D inhibits protein synthesis, it was unexpected that no homology was found between the carboxy‐terminal part of this colicin and that of the protein synthesis inhibiting colicin E3 and cloacin DF13. This could indicate that colicin D does not function in the same manner as the latter two bacteriocins. The observed homology with colicin B supports the domain structure concept of colicin organization. The structural organization of the colicin operon is discussed. The extensive amino‐terminal homology between colicins D and B, and the strong carboxy‐terminal homology between colicins B, A, and N suggest an evolutionary assembly of colicin genes from a few DNA fragments which encode the functional domains responsible for colicin activity and uptake.
Cloing and characterization of an Escherichia coli gene, pcnB, affecting plasmid copy number
Authors: March J. B. , Colloms M. D. , Hart‐Davis D. , Oliver I. R. , Masters M. 
Published: October 2006

SummaryA gene, pcnB, affecting the copy number of ColE1‐related plasmids has been cloned and mapped to 3.6 min on the Escherichia coli chromosome between panD and fhu. The gene encodes a previously un‐described 48 kD protein. Several independently isolated mutants exhibiting the same phenotye, reduced copy number, have been shown to be pcnB.
Cloning and analysis of a deletable tetracycline‐resistance determinant of Streptomyces lividans 1326
Authors: Kessler A. , Dittrich W. , Betzler M. , Schrempf H. 
Published: October 2006

SummaryAn unstable determinant encoding resistance to tetracycline and minocycline has been cloned and characterized. It could be demonstrated that this determinant shares extensive homology with the otrA gene identified in Streptomyces rimosus. Tetracycline‐sensitive variants of Streptomyces lividans derive mostly by deletion of this resistance determinant and neighbouring DNA regions.
Extensive sequence homology between IgA receptor and M proteins in Streptococcus pyogenes
Authors: Frithz E. , Hedén L.‐O. , Lindahl G. 
Published: October 2006

SummaryMany strains of Streptococcus pyogenes are known to express a receptor for IgA. The complete nucleotide sequence of the gene for such a receptor, protein Arp4, has been determined. The deduced amino acid sequence of 386 residues includes a signal sequence of 41 amino acids and a putative membrane anchor region, both of which are homologous to similar regions in other streptococcal surface proteins. The processed form of the IgA receptor has a length of 345 amino acids and a calculated molecular weight of 39544. The N‐terninal sequence of the processed form is different from that previously found for a similar IgA receptor isolated from a S. pyogenes strain of type M60. The sequence of protein Arp4 shows extensive homology to the C‐terminal half of streptococcal M proteins, but not to the streptococcal IgG receptor protein G or staphlyococcal protein A. Apart from the membrane anchor, this homology includes a sequence of 119 amino acid residues containing three repeated units and a 54‐residue sequence without repeats. The protein expressed in Escherichia coli is found in the periplasmic space, in which it constitutes the major protein. Protein Arp4 is the first example of a surface protein that has both immunoglobulin‐binding capacity and structural features characteristic of M proteins. And structural features characteristic of MJ proteins.
The role of the cell surface in social and adventurous behaviour of myxobacteria
Authors: Shimkets L. J. 
Published: October 2006

SummaryThe myxobacteria are an unusually social group of prokaryotic organisms that form fruiting bodies containing dormant myxospores in response to nutritional stress. Social behaviour is controlled by a multigene system known as ‘S’ and by a series of intercellular signals that are released during development. The genes controlling these communication systems have been identified by mutational analysis and current research is directed toward examining the functions of these genes. S− mutants are generally nondevelopmental and noncohesive. They lack pili, a Congo red receptor, and 50‐nm‐wide fibrils which extend outward from the ceil surface. Changes in the architecture of the cell surface have been studied by means of surface labelling and with monoclonal antibodies directed against cell‐surface antigens. The cell surface undergoes dramatic changes during the course of development. Most vegetative antigens decrease in concentration or disappear completely while new development‐specific antigens appear.
Fine‐tuning of nif and fix gene expression by upstream activator sequences in Bradyrhizobium japonicum
Authors: Gubler M. 
Published: October 2006

SummaryThe significance of Bradyrhizobium japonicum upstream activator sequences (UASs) for differential NifA‐mediated fix and nif gene expression was investigated by two means: (i) hybrid fixA‐ and fixB‐lacZ fusions were constructed by transposing a nifH‐UAS cartridge in front of their promoters; and (ii) B. japonicum mutants were generated carrying specific chromosomal deletions or UAS cartridge insertions within the fixA, fixB or nifH promoter‐upstream regions. Expression of fixA was not affected, and expression of fixB decreased only to 42%, when the respective fixA and fixB promoter‐upstream DNAs were deleted. This shows that in B. japonicum the Njf A‐dependent activation of at least the fixA promoter does not require the presence of a closely adjacent UAS. Deletion of the UASs in front of the nifH gene not only reduced the expression of nifH down to 2.5% but, surprisingly, also resulted in a reduction of the fixB mRNA level to less than 20%. This suggests that the nifH‐UASs may exert a long‐range effect on the expression of the 3‐kb‐distant fixBCX operon in nif cluster I of B. japonicum. Artificial transposition of the nif‐UASs in front of the fixA and fixB promoters strongly enhanced fixA and fixB expression.
Characterization of a cis regulatory DNA element necessary for formate induction of the formate dehydrogenase gene (fdhF) of Escherichia coli
Authors: Birkmann A. , Bock A. 
Published: October 2006

SummaryThe fdhF gene, encoding the selenopolypeptide of formate dehydrogenase (FDHH). has a ‐12/‐24 nif‐type consensus promoter. A cis‐acting DNA element, which is required for the regulation of the promoter by formate under anaerobic conditions, has been identified. This regulatory sequence of about 25bp in length is located 110 bp upstream of the transcription start site. By analysing a variety of mutant constructs in this region (5’deletions, internal deletions and point mutations) we were able to identify a hexanucleotide sequence ‐GTCACG‐, which is important for the formate regulation of the fdhF promoter. The data also indicate that this element has many of the properties characteristic of eukaryotic enhancers.
Molecular cloning and characterization of chromosomal virulence region kcpA of Shigella flexneri
Authors: Yamada M. , Sasakawa C. , Okada N. , Makino S.‐I. , Yoshikawa M. 
Published: October 2006

SummaryIn Shigella flexneri, in addition to several well‐recognized plasmid‐borne virulence loci, at least three genetic loci implicated in pathogenesis have been recognized on the chromosome. To understand more about the pathogenesis of bacillary dysentery at a molecular level, the genetically recognized but previously unidentified KcpA region (one of the chromosomal regions near purE) was cloned and sequenced. A single translatable open reading frame encoding a 12310 Dalton protein corresponding to the minicell product was found. Immunofluorescence microscopy, as well as optical and electron microscopic comparison of tissue‐cultured cells and guinea‐pigs’eyes infected with wild‐type or kcpA mutant bacteria, revealed that the kcpA product is required by invading bacteria for spread into adjacent cells.