bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleotide sequence of the structural gene for class I pilin from Neisseria meningitidis: homologies with the pilE locus of Neisseria gonorrhoeae
Authors: Potts W. J. , Saunders J. R. 
Published: October 2006

SummaryThe nucleotide sequence has been determined for the expressed pilin (pilE) locus of Neisseria meningitidis strain C311 which produces class I pili that areantigenically and structurally similar to those of gonococci. The deduced amino acid sequence of the N. meningitidis pilE translation product contains a 7amino acid N‐terminal pre‐pilin leader sequence which is identical to that found in gonococcal pilin and which is characteristic of N‐methylphenylalanine pili in general. The succeeding N‐terminal 53 amino acids are identical to those found in the equivalent position in antigenically variant gonococcal pilins and confirm direct peptide sequencing of the amino‐terminus of atleast one type of meningococcal pilin. Other regions that are conserved in variant pilin potypeptides from Neisseria gonorrhoeae are conserved at the aminoacid level in the class I meningococcal pilin but the coding DNA contains numerous base substitutions when compared with the equivalent gonococcal pH sequence. Sequences extending downstream for about 140bp on the 3′ side of the coding region for both pilin genes are only about 85% homologous.
Epitope mapping with solid‐phase peptides: identification of type‐, subspecies‐, species‐ and genus‐reactive antibody binding domains on the major outer membrane protein of Chlamydia trachomatis
Authors: Conlan J. W. , Clarke I. N. , Ward M. E. 
Published: October 2006

SummaryThe major outer membrane protein (MOMP) of Chlamydiatrachomatis carries serovar‐, subspecies‐, species‐ and genus immunodomains, antibodies to which may be protective. We have compared the inferred amino acid sequences for MOMP from different servoars of C. trachomatis and from Chlamydia psittaci to identify the likely locations of these sero‐taxonomic epitopes. Overlapping peptides corresponding to each of these regions were synthesized on a solid phase and probed with monoclonal antibodies (MAbs) of appropriate specificities. We describe the primary structures of the binding sites of MAb to each of these four epitopes on C. trachomatis serovarL1 MOMP
High‐level expression and epitope localization of the major outer membrane protein of Chlamydia trachomatis serovar L1
Authors: Pickett M. A. , Ward M. E. , Clarke I. N. 
Published: October 2006

SummaryFragments of the gene encoding the major outer membrane porin protein (MOMP) of Chlamydia trachomatis serovar L1 were ligated into the pUC plasmid vectors to give a series of overlapping recombinant sex pressing MOMP from the lac promoter. Induction of this promoter with IPTG leads to high‐level expression of the recombinant porin protein. Electron microscopy shows the presence of insoluble inclusions within the Escherichia coli host cells. Probing the expressed MOMP fragments with a set of monoclonal antibodies permitted localization of the four binding sites (epitopes)of primary‐sequence‐dependent monoclonal antibodies that exhibit genus‐, species‐, subspecies and type (serovar)‐specific reactivities.
Structure of the gene for the transition state regulator, abrB: regulator synthesis is controlled by the spo0A sporulation gene in Bacillus subtilis
Authors: Perego M. , Spiegelman G. B. , Hoch J. A. 
Published: October 2006

SummarySporulation begins coincidentally with the expression of several stationary‐phase‐associated gene products during the transition state of a culture from exponential to stationary phase. Mutations in the stage 0 sporulation genes prevent the expression of these gene products in addition to blocking sporulation. Suppressor mutations in the abrB gene, in a spo0 background, restore stationary‐phase‐associated gene expression but not sporulation. The nature of the abrB gene product was investigated by isolating and sequencing the abrB gene. The abrB gene coded for a 96‐amino‐acid protein (molecular weight 10773) and contained a helix‐turn‐helix structure common to DNA binding proteins. Analysis of expression of the abrB gene using lacZ transcription fusions and direct measurement of mRNA content by hybridization showed that the spo0A gene repressed transcription of the abrB gene. Primer extension analysis of abrB gene mRNA revealed two initiation sites. The downstream site was dramatically repressed in spo0A+ strains, while the upstream site appeared not to be regulated by spo0A. Five abrB mutant alleles were cloned and sequenced. One mutation, abrB 4, resided within the structural gene and continued to overexpress abrB messenger RNA from both promoters. A promoter mutation, abrB 15, reduced transcription from the downstream promoter but not the upstream promoter. Thus, the phenotype of abrB mutations results from inactivation of the abrB gene product or by prevention of its overexpression. The results suggest that the abrB gene codes for a regulator which controls several genes whose products are normally produced during the transition phase between active growth and sporulation. The level of this regulator is, in turn, controlled by the spo0A gene. The pleiotropic phenotypes of spo0A mutants result from uncontrolled overexpression of the abrB regulator.
Identification of the protein encoded by rodC, a cell division gene from Bacillus subtilis
Authors: Honeyman A. L. , Stewart G. C. 
Published: October 2006

SummaryThe rodC 1 mutation of Bacillus subtilis is a temperature‐sensitive marker which affects the orientation of the plane of cell division. We have cloned the rodC gene and have localized the site of the rodC 1 lesion. To identify the rodC gene product, we have subjected several plasmid clones containing B. subtilis chromosomal DNA from the rodC region to maxicell analysis in Escherichia coli. A 68 kiloDalton protein has been identified as the rodC gene product. This is the initial cloning of a cell division gene and the identification of its product from B. subtilis. The rodC gene has also been implicated as being directly associated with the synthesis of glycerol teichoic acid.
Nucleotide sequence of the ugp genes of Escherichia coli K‐12: homology to the maltose system
Authors: Overduin P. , Boos W. , Tommassen J. 
Published: October 2006

SummaryThe nucleotide sequence of the ugp genes of Escherichia Coli K‐12, which encode a phosphate‐limitation inducible uptake system for sn‐glycerol‐3‐phosphate and glycerophosphoryl diesters, was determined. The genetic organization of the operon differed from previously published results. A single promoter, containing a putative pho box, was detected by S1‐nuclease mapping. The promoter is followed by four open reading frames, designated ugpB, A, E and C, which encode a periplasmic binding protein, two hydrophobic membrane proteins and a protein that is likely to couple energy to the transport system, respectively. The sequences of the proteins contain the characteristics of several other binding protein‐dependent transport systems, but they seem to be particularly closely related to the maltose system.
Three copies of a single protein II‐encoding sequence in the genome of Neisseria gonorrhoeae JS3: evidence for gene conversion and gene duplication
Authors: van der Ley P. 
Published: October 2006

SummaryGonococci express a family of related outer membrane proteins designated protein II (P.II). These surface proteins are subject to both phase variation and antigenic variation. The P.II gene repertoire of Neisseria gonorrhoeae strain JS3 was found to consist of at least ten genes, eight of which were cloned. Sequence analysis and DNA hybridization studies revealed that one particular P.II‐encoding sequence is present in three distinct, but almost identical, copies in the JS3 genome. These genes encode the P.II protein that was previously identified as P.IIc. Comparison of their sequences shows that the multiple copies of this P.IIc‐encoding gene might have been generated by both gene conversion and gene duplication.
Three α‐amylase genes of Aspergillus oryzae exhibit identical intron‐exon organization
Authors: Wirsel S. , Lachmund A. , Wildhardt G. , Ruttkowski E. 
Published: October 2006

SummaryWe have cloned three genes (amy1, amy2 and amy3) encoding α‐amylase in the filamentous fungus Aspergillus oryzae. The established overall sequences have a very high degree of homology, showing divergences mainly in the 3’‐untranslated regions. The positions and the sequences of the eight introns were found to be absolutely identical in the three genes. The sequence analysis of the 5’‐regions revealed presumptive TATA, CAAT and GC boxes. Primer extension analysis was performed to determine the transcription start. We were able to detect mRNAs from amy1 and amy3 but not from amy2 with gene‐specific oligonucleotide probes complementary to the 3’‐noncoding regions.
Transformation of Mycobacterium smegmatis with Escherichia coii plasmids carrying a selectable resistance marker
Authors: Zainuddin Z. F. , Kunze Z. M. , Dale J. W. 
Published: October 2006

SummaryOne limiting factor in studies of tuberculosis and leprosy is the difficulty of genetic analysis and manipulation of mycobacteria. Two approaches were adopted for the construction of vectors, based on different Escherichia coli plasmids and using Mycobacterium smegmatis as the host. In both cases we found that the original E. coli plasmid is capable of being replicated in M. smegmatis, yielding chloramphenicol‐resistant colonies. One such plasmid has been recovered from a M. smegmatis transformant and used to re‐transform both M. smegmatis and E. coli to chloramphenicol resistance. This plasmid is indistinguishable from the original plasmid by restriction analysis, and can be used as a shuttle vector for the genetic manipulation of mycobacterial species.
Partial nucleotide sequence of the pts operon in Salmonella typhimurium: comparative analyses in five bacterial genera
Authors: Schnierow B. J. , Yamada M. , Saier M. H. 
Published: October 2006

SummaryThe nucleotide sequence of a Salmonella typhimurium DNA segment of 549 base pairs which encompasses the operator‐promoter of the pts operon, the entirety of the ptsH gene, encoding HPr of the phosphotransferase system (PTS), the first 29 nucleotides of the ptsl gene, encoding Enzyme I of the PTS, and the intercistronic region between the ptsH and ptsl genes was determined and compared with the corresponding sequence from Escherichia coli (De Reuse et al., 1985). The two sequences showed 91 % overall identity, with some regions showing sequence conservation and others exhibiting relative divergence. Two open reading frames were identified in both species: one encoded HPr on the ‘sense’ strand (255 nucleotides; 12 nucleotide differences, no amino acid differences); the other, on the anti‐sense strand, consisted of 291 nucleotides (13 nucleotide differences, 13 amino acid differences). While HPr bears a net negative charge, the putative protein encoded by the open reading frame on the anti‐sense strand is strongly basic.Computer analyses of HPr proteins from five different bacterial genera revealed four regions which show strong sequence identity and therefore are presumed to be critical for maintenance of biological activity. Two of these regions were specific to Gram‐positive bacteria. Proposed functions for each of these regions are discussed. Relative evolutionary distances between the HPr proteins were also computed.
Genetics of pertussis toxin
Authors: Gross R. , Aricò B. , Rappuoli R. 
Published: October 2006

SummaryPertussis toxin (PT) is the major virulence factor of Bordetella pertussis. The cloning and nucleotide sequencing of the PT genes from B. pertussis, Bordetella parapertussis and Bordetella bronchiseptica has elucidated the evolution of the Bordetella species and allowed considerable advances towards the understanding of their gene expression and the development of safer vaccines against pertussis.
Identification of amino acid sequences that can function as translocators of β‐lactamase in Escherichia coli
Authors: Zhang Y. , Broome‐Smith J. K. 
Published: October 2006

SummaryA plasmid vector, pYZ1, was constructed which lacks most of the β‐lactamase signal‐peptide coding region, but has a unique EcoRI site spanning codons 2 and 3 of the resultant cytoplasmic β‐lactamase derivative. Short quasi‐random DNA sequences were cloned into the EcoRI site and Escherichia coli transformants in which some translocation of β‐lactamase across the cytoplasmic membrane was restored were selected by their ability to survive and form colonies on plates containing a low level of ampicillin. About 15–20% of all in‐frame inserts restored some β‐lactamase trans‐location and the salient feature of these sequences was their marked hydrophobicity. These results are discussed in the light of a similar study in which sequences able to function as translocators of invertase in yeast were cloned and analysed (Kaiser et al., 1987).
Subcellular localization of proteins encoded by the phenotypically cryptic plasmid of Neisseria gonorrhoeae: biological evidence for outer membrane association of the cppB gene product
Authors: Aalen R. B. , Lossius I. , Gundersen W. B. 
Published: October 2006

SummaryAlmost all clinical isolates of Neisseria gonorrhoeae harbour a plasmid of 4.2 kb with no known function. A genetic model based on the DNA sequence of the plasmid, with ten open reading frames, has been proposed by Korch et al., (1985). To address the question of the function of the encoded proteins, some of which are expressed when the plasmid is harboured by Escherichia coli, the subcellular locations of such proteins were investigated in minicells of Escherichia coli DS410. The protein CppB, earlier proposed to be a membrane‐spanning polypeptide, was found associated with the outer membrane. Up to five other cryptic plasmid proteins were found to be localized in the periplasm.
The gene for a small stable RNA (10Sa RNA) of Escherichia coli
Authors: Chauhan A. K. , Apirion D. 
Published: October 2006

SummaryA gene that codes for a small stable RNA (362 nucleotides) has been sequenced. It is a monocistronic gene, with its own promoter and terminator. It produces a precursor that is about 100 nucleotides longer than the mature RNA with all the extra nucleotides at the 3′ end. The gene contains an open reading frame that corresponds to a small protein 25 amino acids long.
Isolation of α‐tubulin genes from the human malaria parasite, Plasmodium falciparum: sequence analysis of α‐tubulin
Authors: Holloway S. P. , Sims P. F. G. , Delves C. J. , Scaife J. G. , Hyde J. E. 
Published: October 2006

SummaryAs a step towards indentifying exploitable differences between host and parasite at the molecular level, we have isolated and sequenced genomic clones encompassing an entire α‐tubulin gene (designated α‐tubulin I) from the human malaria parasite, Plasmodium falciparum. The gene, which contains two introns, encodes a product with a predicted length of 453 amino acid residues (50.3 kD). The protein sequence shows a high degree of homology to other α‐tubulins, particularly that of the coccidian parasite, Toxoplasma gondii (94%), whose gene carries introns in identical positions. Only one copy of the α‐tubulin I gene itself was found, although a second gene designated α‐II was also identified which is closely related but which differs at both the nucleotide and amino acid sequence levels. The α‐I and β‐tubulin genes were found to reside on different chromosomes.
The nodL gene from Rhizobium leguminosarum is homologous to the acetyl transferases encoded by lacA and cysE
Authors: Downie J. A. 
Published: October 2006

SummaryThe predicted protein sequence of the nodL gene from Rhizobium leguminosarum was screened against translations of the GenBank DNA sequence database. A very strong homology was found to lacA, which encodes thiogalactoside transferase; homology between NodL and the cysE gene product (serine acetyl transferase) was also found. Comparison of the conserved regions of the three protein sequences indicated a domain that may be an active site of the enzymes.
Families of bacterial signal‐transducing proteins
Authors: Gross R. , Aricò B. , Rappuoli R. 
Published: October 2006

SummaryBacteria can respond to a variety of environmental stimuli by means of systems generally composed of two proteins. The first protein (sensor or transmitter) is usually a transmembrane protein with cytoplasmic and extracytoplasmic domains. The extracytoplasmic domain (sensor) senses the environment and transfers the signal through the transmembrane domain to the cytoplasmic domain (transmitter), which has kinase activity. The second protein is located in the cytoplasm and contains an amino‐terminal domain (receiver), which can be phosphorylated by the transmitter, and a carboxy‐terminal region (regulator), which regulates gene expression by binding to DNA. The transmitter and receiver modules (the kinase and its target) are conserved in all signal‐transducing systems and are the‘core structure’of this two‐component system. The sensors and the regulators vary according to the stimuli they respond to and the DNA structure they interact with. On the basis of their sequence homology, the proteins belonging to such two‐component systems can be classified into different families, which are summarized in this review.
Phase variants of Bordetella bronchiseptica arise by spontaneous deletions in the vir locus
Authors: Monack D. M. , Arico B. , Rappuoli R. , Falkow S. 
Published: October 2006

Summary Bordetella bronchiseptica is a common respiratory tract pathogen of many mammalian species. Nucleotide sequences from the iocus involved in coordinate regulation of B. pertussis virulence factors, vir, were shown to have a high degree of homology to chromosomal DNA from virulent (Vir+) and avirulent (Vir−) strains of B. bronchiseptica. Small deletions, 50 bp to 500 bp, within the vir locus were found in some of the Vir− phase variants. The vir locus and the adjacent 5′ portion of the fhaB structural gene were cloned from the parental Vir+B. bronchiseptica strain on a 23.5kb BamHl fragment. Restriction enzyme mapping of the cloned B. bronchiseptica vir locus revealed similarities with and differences from the previously cloned B. pertussis vir locus. The cloned B. bronchiseptica vir locus complemented spontaneous Vir− variants of Bordetella pertussis and B. bronchiseptica as well as wr::Tn5 mutants of B. pertussis. Comparison of various functions of the vir loci of B. bronchiseptica and B. pertussis revealed some interesting differences in the coordinate regulation of virulence factors.
Functional characterization of a putative internal promoter sequence between the 16S and the 23S RNA genes within the Escherichia coli rrnB operon
Authors: Zacharias M. , Wagner R. 
Published: October 2006

SummaryTranscription of ribosomal RNAs in Escherichia coli is started from two strong tandem promoters, P1 and P2. tt is known, however, that internal promoter‐like structures occur and in a recent report (Mankin et al., 1987) a promoter sequence Pi within the 16S and 23S RNA spacer region showing good homology to the pro‐karyotic consensus promoter structure was identified. It was proposed that this putative promoter has a possible function in the transcription of ribosomal RNAs in E. coli. Fusion of various DNA fragments containing the putative promoter sequence and different parts of the 16S/23S spacer region as well as the 23S RNA to the galactokinase gene allowed us to assess the functional activity of the promoter in vivo. To determine any growth rate dependent function of the putative promoter, the measurements were performed under different growth conditions. The promoter activity did not exceed 7% of the lac promoter under in vivo assay conditions. In addition, transcription starting at the promoter Pi did not proceed through the entire 23S RNA gene. We conclude, therefore, that transcription from Pi does not contribute significantly to the synthesis of ribosomal RNAs. Thus Its functional significance, if any, remains elusive.
The biochemical basis for growth inhibition by L‐phenylalanine in Neisseria gonorrhoeae
Authors: Bhatnagar R. K. , Berry A. , Hendry A. T. , Jensen R. A. 
Published: October 2006

SummaryClinical isolates of Neisseria gonorrhoeae are commonly subject to growth inhibition by phenylpyruvate or by L‐phenylalanine. A blockade of tyrosine biosynthesis is indicated since inhibition is reversed by either L‐tyrosine or 4‐hydroxyphenylpyruvate. Phenylalanine‐resistant (PheR) and phenylalanine‐sensitive (Phes) isolates both have a single 3‐deoxy‐D‐arabino‐heptulosonate 7‐phosphate (DAHP) synthase that is partially inhibited by L‐phenylalanine (80%). However, PheS and PheR isolates differ in that the ratio of phenylpyruvate aminotransferase to 4‐hydroxyphenylpyruvate aminotransferase is distinctly greater in PheS isolates than in PheR isolates. A mechanism for growth inhibition is proposed in which phenylalanine exerts two interactive effects, (i) Phenylalanine decreases precursor flow to 4‐hydroxyphenylpyruvate through its controlling effect upon DAHP synthase; and (ii) phenylalanine is largely transaminated to phenylpyruvate, which saturates both aminotransferases, preventing transamination of an already limited supply of 4‐hydroxyphenylpyruvate to L‐tyrosine.
Integration of the Serratia marcescens haemolysin into human erythrocyte membranes
Authors: Schiebel E. , Braun V. 
Published: October 2006

SummaryThe haemolytic activity of Serratia marcescens is determined by two proteins, ShIA and ShIB. ShIA integrates into the erythrocyte membrane and causes osmotic lysis through channel formation. The conformation of ShIA and its interaction with erythrocyte membranes were studied by determining the cleavage of ShIA by added trypsin. Our results suggest that the conformation of inactive ShIA (from an ShIB− strain) differs from the active ShIA, and that in a hydrophobic environment (detergent or membrane) active ShIA assumes a conformation distinct from that in buffer. Only active haemolysin adsorbed to erythrocytes. ShIA was firmly integrated into the erythrocyte membrane since it was only released under conditions which also dissolved the integral erythrocyte membrane proteins. Moreover, ShIA integrated into ‘ghosts’ remained there and was not haemolytic when incubated with erythrocytes. From the trypsin cleavage pattern obtained with haemolysin and C‐terminally truncated, but still active, haemolysin derivatives integrated into erythrocytes, and sealed and unsealed erythrocyte ‘ghosts’, we conclude that ShiA is preferentially cleaved by trypsin at a few sites but only from the inside of the erythrocyte. Haemolysin in the erythrocyte membrane forms a water‐filled channel and is resistant to trypsin and other proteases.
The Escherichia coli protein, Fis: specific binding to the ends of phage Mu DNA and modulation of phage growth
Authors: Bétermier M. , Lefrère V. , Koch C. , Alazard R. , Chandler M. 
Published: October 2006

SummaryWe show, using gel retardation, that crude Escherichia coli cell extracts contain a protein which binds specifically to DNA fragments carrying either end of the phage Mu genome. We have identified this protein as Fis, a factor involved in several site‐specific recombinational switches. Furthermore, we show that induction of a Mucte62 prophage in a fis lysogen occurs at a lower temperature than that of a wild‐type strain, and that spontaneous induction of Mucfs62 is increased in the fis mutant. DNasel footprinting using either crude extracts or purified Fis indicate that binding on the left end of Mu occurs at a site which overlaps a weak transposase binding site. Thus, Fis may modulate Mu growth by influencing the binding of transposase, or other proteins, to the transposase binding site(s), in a way similar to its influence on Xis binding in phage λ.