bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and characterization of ppiB, a Bacillus subtilis gene which encodes a cyclosporine A‐sensitive peptidyl‐prolyl cis‐trans isomerase
Authors: Herrler Michael , Bang Holger , Marahiel Mohamed A. 
Published: October 2006

SummarySequencing of N‐terminal and internal peptide fragments of the purified 17kDa Bacillus subtilis peptldyl‐prolyl cls‐trans isomerase (PPlase) revealed sequence identity to conserved regions of a number of eukaryotic and prokaryotic cyclophilins. Using two oligonucleotide primers corresponding to the N‐terminus and a highly conserved internal amino acid sequence, polymerase chain reactions (PCR) with B. subtilis genomic DNA were carried out. The resultant PCR fragment of 335 bp was cloned, sequenced and subsequently used as a probe for screening a λZap II gene library of B. subtilis. Two overlapping positive clones of 5 and 7 kb containing the B. subtilis PPlase gene (ppiB), which is 432 bp in length and encodes a protein of 144 amino acid residues, were identified and two distinct transcriptional initiation sites at the 5′ end of ppiB were mapped. The entire region (35 kb) between spoVA and serA was recently sequenced in B. subtilis, and an open reading frame (ORF) that encodes a putative peptidyl‐prolyl cis‐trans isomerase at about 210° on the B. subtilis genetic map was located. This putative PPlase is identical to PPiB. We have overexpressed the ppiB gene in Escherichia coli, purified the encoded protein to apparent homology and shown that it exhibits PPlase activity. In addition, the recombinant PPiB shows a significant inhibition of PPlase activity by cyclosporin A (CsA) at a level comparable to that observed for the B. subtilis enzyme. Interestingly the B. subtilis PPlase shows about 40% identity to eukaryotic PPlases and less similarity to those of Gram‐negative bacteria (27–32% identity). Like other interruption mutants of yeast and Neurospora, which iack a functionai cyclophilin gene, a B. subtiiis mutant containing ppiBv.cat, a caf‐interrupted copy of ppiB in the chromosome, is viable.
Interaction of the Chlamydia trachomatis histone H1‐like protein (Hc1) with DNA and RNA causes repression of transcription and translation in vitro
Authors: Pedersen Lotte Bang , Birkelund Svend , Christiansen Gunna 
Published: October 2006

SummaryThe 18 kDa histone H1‐like protein from Chlamydia trachomatis (Hc1) is a DNA–binding protein thought to be involved in condensation of the chlamydial chromosome during late stages in the chlamydial life cycle. Expression of Hc1 in Escherichia coli results in an overall relaxation of DNA and severely affects DNA, RNA and protein synthesis. We have analysed the interaction of Hc1 with single‐stranded DNA and RNA by Southwestern and Northwestern blotting. Furthermore, we show that purified, recombinant Hc1 dramatically affects transcription and translation in vitro at physiologically relevant concentrations. These results were found to coincide with the formation of condensed Hc1–DNA and Hc1–RNA complexes as revealed by agarose gel electrophoresis and electron microscopy. The implications of these results for possible functions of Hc1 in vivo are discussed.
The Pseudomonas fluorescens lipase has a C‐terminal secretion signal and is secreted by a three‐component bacterial ABC‐exporter system
Authors: Duong Frank , Soscia Chantal , Lazdunski Andrée , Murgier Maryse 
Published: October 2006

SummaryBoth Pseudomonas aeruginosa and Pseudomonas fluorescens secrete a lipase into the extracellular medium. Unlike the lipase of P. aeruginosa, the lipase produced by P. fluorescens does not contain any N‐terminal signal sequence. We show that the P. fluorescens lipase is secreted through the signal peptide‐independent pathway of the alkaline protease that we previously identified in P. aeruginosa. Secretion of this protease (AprA) is dependent on the presence of three genes located adjacent to the aprA gene, aprD, aprE and aprF. The three secretion functions permit an efficient secretion of P. fluorescens lipase. Inactivation of one of them (AprE) prevented this secretion. In Escherichia coli, the three proteins AprD, AprE, AprF are necessary and sufficient for efficient secretion of lipase to the extracellular medium. The secretion signal is located within the C‐terminal part of the lipase sequence and can promote efficient secretion of a passenger protein. Thus the P. fluorescens lipase secretion system belongs to the group of the three‐component bacterial ABC‐exporter systems.
pecS: a locus controlling pectinase, cellulase and blue pigment production in Erwinia chrysanthemi
Authors: Reverchon Sylvie , Nasser William , Robert‐Baudouy Janine 
Published: October 2006

Summary Erwinia chrysanthemi mutants (designated as pecS) displaying derepressed pectate lyase and cellulose synthesis were isolated. In addition, the pecS mutation is responsible for production of an extracellular insoluble blue pigment whose synthesis is cryptic in the wild‐type 3937 strain. Transduction analysis indicates that the phenotype is due to a single mutation located near the xyl marker on the strain 3937 chromosome. This mutation was complemented by an R‐prime plasmid carrying the xyl and argG genes of E. chrysanthemi, suggesting that the pecS product acts in trans to modulate pectinase, cellulase and blue pigment production. Insertion mutagenesis of the cloned region and recombination of the corresponding mutations in the bacterial chromosome by marker exchange revealed the existence of two divergently transcribed genes, pecS and pecM, that are both involved in the pectate lyase and cellulase regulation. The nucleotide sequences of pecS and pecM were determined. The pecS gene encodes a 166 amino acid polypeptide that shows similarity to the MprA regulatory protein of Escherichia coli whereas the pecM gene encodes a 297 amino acid polypeptide that was shown to be an integral membrane protein. The possible functions of the PecS and PecM proteins derived from the mutant phenotype and sequence analysis are discussed in terms of signal transduction and transcription regulation.
Cloning of the nupC gene of Escherichia coli encoding a nucleoside transport system, and identification of an adjacent Insertion element, IS 186
Authors: Craig Jane E. , Zhang Yianbiao , Gallagher Maurice P. 
Published: October 2006

Summary Escherichia coli is known to contain more than one active transport system for nucleoside uptake. In the present study we report the sequence of a gene encoding a second nucleoside transport system, nupC (in addition to nupG.) An open reading frame (ORF) of 1200bp was identified that codes for a hydrophobic polypeptide of 43 560 Da and an NupC fusion protein was shown to be membrane associated. The native NupC protein is also identified, following over‐expression. NupC exhibits short regions of homology to several membrane‐associated proteins, including LacY and Cyd. Analysis of the nupC promoter region revealed the presence of at least two putative CRP‐binding sites, centred at–40bp and–89bp, which probably flank a CytR‐binding site. In addition, an adjacent IS186 element was identified and found to reside within a putative terminator structure, downstream from the nupC ORF. This arrangement is shown to reflect the previously established gene order on the E. coli chromosome.
TMAO anaerobic respiration in Escherichia coli: involvement of the tor operon
Authors: Méjean Vincent , Lobbi‐Nivol Chantal , Lepelletier Michèle , Giordano Gérard , Chippaux Marc , Pascal Marie‐Claire 
Published: October 2006

SummaryThe trimethylamine N‐oxide (TMAO) respiratory system is subject to a strict positive control by the substrate. This property was exploited in the performance of miniMu replicon‐mediated in vivo cloning of the promoter region of gene(s) positively regulated by TMAO. This region, located at 22 min on the chromosome, was shown to control the expression of a transcription unit composed of three open reading frames, designated torC, torA and torD, respectively. The presence of five putative c‐type haem‐binding sites within the TorC sequence, as well as the specific biochemical characterization, indicated that torC encodes a 43 300 Da c‐type cytochrome. The second open reading frame, torA, was identified as the structural gene for TMAO reductase. A comparison of the predicted amino‐terminal sequence of the torA gene product to that of the purified TMAO reductase indicated cleavage of a 39 amino acid signal peptide, which is in agreement with the periplasmic location of the enzyme. The predicted TorA protein contains the five molybdenum cofactor‐binding motifs found in other molybdoproteins and displays extensive sequence homology with BisC and DmsA proteins. As expected, insertions in torA led to the loss of TMAO reductase. The 22 500 Da polypeptide encoded by the third open reading frame does not share any similarity with proteins listed in data banks.
Antigenic drift of non‐encapsulated Haemophilus influenzae major outer membrane protein P2 in patients with chronic bronchitis is caused by point mutations
Authors: Duim Birgitta , van Alphen Loek , Eijk Paul , Jansen Henk M. , Dankert Jacob 
Published: October 2006

SummaryThe sequence of the gene encoding major outer membrane protein (MOMP) P2 of antigenic variants of non‐encapsulated Haemophilus influenzae isolated from persistently infected chronic bronchitis patients was analysed. Antigenic drift was shown to result from single base changes in the P2 gene, all generating amino acid changes in the surface‐exposed loops of MOMP P2, predominantly in loop 6. Similar single base changes were observed in H. influenzae persistently present in a subcutaneous cage implanted in rabbits, as well as in a spontaneous H. influenzae mutant that had survived MOMP P2 specific monoclonal‐antibody‐dependent bactericidal killing in vitro. We hypothesize that accumulation of point mutations under the selection pressure of immunity is a mechanism of antigenic drift of a surface‐exposed protein during persistent H. influenzae infection
DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans
Authors: Minton Kenneth W. 
Published: October 2006

Summary Deinococcus radiodurans and other members of the same genus share extraordinary resistance to the lethal and mutagenic effects of ionizing and u.v. radiation and to many other agents that damage DNA. While it is known that this resistance is due to exceedingly efficient DNA repair, the molecular mechanisms responsible remain poorly understood. Following very high exposures to u.v. irradiation (e.g. 500 Jm−2, which is non‐lethal to D. radiodurans), this organism carries out extremely efficient excision repair accomplished by two separate nucleotide excision repair pathways acting simultaneously. One pathway requires the uvrA gene and appears similar to the UvrABC excinuclease pathway defined in Escherichia coli. The other excision repair pathway is specific for u.v. dimeric photoproducts, but is not mediated by a pyrimidine dimer DNA glycosylase. Instead, it is initiated by a second bona fide endonuclease that may recognize both pyrimidine dimers and pyrimidine‐(6–4)pyrimidones. After high doses of ionizing‐radiation (e.g. 1.5Mrad), D. radiodurans can mend >100 double‐strand breaks (dsb) per chromosome without lethality or mutagenesis. Both dsb mending and survival are recA‐dependent, indicating that efficient dsb mending proceeds via homologous recombination. D. radiodurans contains multiple chromosomes per cell, and it is proposed that dsb mending requires extensive recombination amongst these chromosomes, a novel phenomenon in bacteria. Thus, D. radiodurans may serve as an easily accessible model system for the double‐strand‐break‐initiated interchromosomal recombination that occurs in eukaryotic cells during mitosis and meiosis.
Rhizobium meliloti DctD, a σ54‐dependent transcriptional activator, may be negatively controlled by a subdomain in the C‐terminal end of its two‐component receiver module
Authors: Gu Baohua , Lee Joon H. , Hoover Timothy R. , Scholl Dean , Nixon B. Tracy 
Published: October 2006

Summary Rhizobium meliloti DctD is believed to have three functional domains: an N‐terminal, two‐component receiver domain; and like other σ54‐dependent activators, C‐terminal and central domains for DNA binding and transcription activation. We have characterized a progressive series of M‐terminal deletions of R meliloti DctD. The N‐terminal domain was not needed for binding the dctA upstream activation sequence. Only 25% of the C‐terminal end of the receiver domain was needed to significantly inhibit the central domain, and proteins lacking up to 60% of the N‐terminal end of the receiver domain were‘inducible’in R. meliloti cells. We hypothesize that the W‐terminal two‐thirds of the DctD receiver domain augments and controls an adjacent subdomain for inhibiting the central domain.
A small (2.4 Mb) Bacillus cereus chromosome corresponds to a conserved region of a larger (5.3 Mb) Bacillus cereus chromosome
Authors: Carlson Cathrine Rein , Kolsto Anne‐Brit 
Published: October 2006

SummaryWe have determined the sizes of the chromosomes of six Bacillus cereus strains (range 2.4–4.3 Mb) and constructed a physical map of the smallest B. cereus chromosome (2.4 Mb). This map was compared to those of the chromosomes of four B. cereus strains and one B. thuringiensis strain previously determined to be 5.4‐6.3 Mb. Of more than 50 probes, 30 were localized to the same half of the larger B. cereus and B. thuringiensis chromosomes. All 30 were also present on the small chromosome. Twenty of the probes present on the other half of the larger chromosomes were either present on extrachromosomal DNA, or absent from the B. cereus strain carrying the small chromosome. We propose that the genome of B. cereus and B. thuringiensis has one constant part and another less stable part which is more easily mobilized into other genetic elements. This part of the genome is localized to one region of the chromosome and may be subject to deletions or more frequent relocations between the chromosome and episomal elements of varying sizes up to the order of megabases.
The energetics of bacterial growth: a reassessment
Authors: Neijssel Oense M. , de Mattos M. Joost Teixeira 
Published: October 2006

SummaryThe growth yield of microbial cultures can be used to estimate the efficiency of energy generation during a fermentation or respiration, in the past, the assessment of this efficiency in organisms carrying out a respiration has been the subject of many heated debates. This has partly been caused by the complexity of microbial respiratory chains. Strains of Escherichia coli specifically modified in their respiratory chain have been used recently to re‐evaluate the energetic efficiency of the bacterial respiration using chemostat cultures. The different strains indeed show different growth efficiencies. The physiological significance of energetically less‐efficient branches of the respiratory chain is discussed.
The terminal oxidases of Paracoccus denitrificans
Authors: de Gier Jan‐Willem L. , Lübben Mathias , Reijnders Willem N. M. , Tipker Corinne A. , Slotboom Dirk‐Jan , van Spanning Rob J. M. , Stouthamer Adriaan H. , van der Oost John 
Published: October 2006

SummaryThree distinct types of terminal oxidases participate in the aerobic respiratory pathways of Paracoccus denitrificans. Two alternative genes encoding sub unit I of the aa3‐type cytochrome c oxidase have been isolated before, namely ctaDI and ctaDII. Each of these genes can be expressed separately to complement a double mutant (ActaDI, ActaDII), indicating that they are isoforms of subunit I of the aa3‐type oxidase. The genomic locus of a quinol oxidase has been isolated: cyoABC. Thisprotohaem‐containing oxidase, called cytochrome bb3, is the oniy quinoi oxidase expressed under the conditions used, in a triple oxidase mutant (ActaDI, ActaDII, cyoB::KmR) an alternative cyto‐chrome c oxidase has been characterized; this cbb3‐type oxidase has been partially purified. Both cytochrome aa3 and cytochrome bb3 are redox‐driven proton pumps. The proton‐pumping capacity of cytochrome cbb3 has been analysed; arguments for and against the active transport of protons by this novel oxidase complex are discussed.
A novel, small endoglucanase gene, egl5, from Trichoderma reesei isolated by expression in yeast
Authors: Saloheimo Anu , Henrissat Bernard , Hoffrén Anna‐Marja , Teleman Olle , Penttilä Merja 
Published: October 2006

SummaryA method is presented for the isolation of genes encoding hydrolytic enzymes without any knowledge of the corresponding proteins. cDNA made from the organism of interest is cloned into a yeast vector to construct an expression library in the yeast Saccharomyces cerevisiae. Colonies producing hydrolytic enzymes are screened by activity plate assays. In this work, we constructed a yeast expression library from the filamentous fungus Trichoderma reesel and isolated a new β‐1,4‐endoglucanase gene on plates containing β‐glucan. This gene, eg15, codes for a previously unknown small protein of 242 amino acids. Despite its small size, the protein contains two conservative domains found in Trichoderma cellulases, namely the cellulose‐binding domain (CBD) and the iinker region that connects the CBD to the catalytic core domain. Molecular modelling of the EGV CBD revealed some interesting structural differences compared to the CBD of the major celluiase CBHI from T. reesei. The catalytic core of EGV is unusually small for a ceiiulase and represents a new family of ceilulases (Family K) and of glycosyl hydrolases (Famlly 45) together with the endoglucanase B of Pseudomonas fluorescens and the endoglucanase V of Humicola insolens on the basis of hydrophobic ciuster anaiysis.
Separate pathways for excision and processing of 16S and 23S rRNA from the primary rRNA operon transcript from the hyperthermophilic archaebacterium Sulfolobus acldocaldarius: similarities to eukaryotic rRNA processing
Authors: Durovic Peter , Dennis Patrick P. 
Published: October 2006

SummaryIn the hyperthermophilic archaebacterium Sulfolobus acidocaldarius, the mature 16S and 23S rRNA are generated by processing of a 5000‐nucleotide transcript. Analysis of intermediates that accumulate in vivo indicates that the transcript contains 11 separate processing sites. The processing and maturation of 23S rRNA appears to follow the typical archaebacterial pathway, utilizing a bulge‐helix‐bulge motif within the 23S processing helix as the substrate for an excision endonuclease. The precursor 23S rRNA that is released is trimmed at its 5′ and 3′ ends to generate the mature 23S rRNA found in 50S ribosomal subunits. The pathway for processing and maturation of 16S rRNA is distinctive and does not use the bulge‐helix‐bulge motif in the 165 processing stem, instead, the transcript is cleaved at several novel positions in the 5′ leader and in the 3′ intercistronic sequence. The excised precursor 16S is trimmed at the 5′ end but an extra 60 nucieotides of what is normally spacer sequence is retained at the 3′ end. The elongated 16S rRNA is present in active 30S subunits. An in vitro processing system for the 16S rRNA has been established. The RNA substrate containing the entire 144‐nucieotide 5′ leader and the first 72 nucleotides of 16S sequence is cleaved at the same positions observed in vivo by an endonuclease activity present in cell extract. These resuits demonstrate (i) that the 16S processing helix is neither utilized nor required for leader processing, and (ii) that complete maturation to the 5′ end of 16S rRNA can occur in the absence of concomitant ribosome assembly and in the absence of all but the first 72 nucleotides of the 16S rRNA sequence. The endonuclease activity responsible for cleavage of the 5′ leader substrate is sensitive to nuclease digestion, suggesting that it contains an essential RNA component. The cleavage sites appear to be located within regions of irregular secondary structure and have a consensus sequence of GAUUCC.
Multiple signalling systems controlling expression of luminescence in Vibrio harveyi: sequence and function of genes encoding a second sensory pathway
Authors: Bassler Bonnie L. , Wright Miriam , Silverman Michael R. 
Published: October 2006

SummaryDensity‐dependent expression of luminescence in Vibrio harveyl is regulated by the concentration of extracellular signal molecules (autoinducers) in the culture medium. One signal‐response system is encoded by the luxL,M,N locus. The luxL and luxM genes are required for the production of an autoinducer (probably β‐hydroxybutryl homoserine lactone), and the luxN gene is required for the response to that autoinducer. Analysis of the phenotypes of LuxL,M and N mutants indicated that an additional signal‐response system also controls density sensing. We report here the identification, cloning and analysis of luxP and luxQ, which encode functions required for a second density‐sensing system. Mutants with defects in luxP and luxQ are defective in response to a second autoinducer substance. LuxQ, like LuxN, is similar to members of the family of two‐component, signal transduction proteins and contains both a histidine protein kinase and a response regulator domain. Analysis of signalling mutant phenotypes indicates that there are at least two separate signal‐response pathways which converge to regulate expression of luminescence in V. harveyl.
traJ sense RNA initiates at two different proMolers in R100‐1 and forms two stable hybrids with antisense finP RNA
Authors: Dempsey Walter B. 
Published: October 2006

SummaryRNase protection experiments show that the sizes of the two R100 finP molecules are 74 and 135 nucleotides. In an RNase III mutant, finP transcripts form stable double‐stranded hybrids of 108bp and 68 bp with traJ transcripts. RNase protection experiments also show that most R100‐1 transcripts originating in traM cross the traM‐traJ intergenic region and end inside the untranslated leader region of traJ. Some extend into the traJ open reading frame. These findings mean that the antisense finP RNA, thought to regulate traJ translation, must regulate traJ transcripts from both J and M proMolers.
Analysis of five tyiosin biosynthetic genes from the tyllBA region of the Streptomyces fradiae genome
Authors: Merson‐Davies Louise A. , Cundiiffe Eric 
Published: October 2006

SummaryThe tyllBA region of the tylosin biosynthetic gene cluster of Streptomyces fradiae contains at least five open reading frames (ORFs). ORF1 {tyll) encodes a cytochrome P450 and mutations in this gene affect macrolide ring hydroxylation. The product of 0RF2 (tylB) belongs to a widespread family of proteins whose functions are speculative, although tylB mutants are defective in the biosynthesis or addition of mycaminose during tylosin production. ORFs 3 and 4 (tylA1 and tylA2) encode δTDP‐giucose synthase and δTDP‐glucose dehydratase, respectively, enzymes responsible for the first two steps common to the biosynthesis of all three deoxyhexose sugars of tylosin via the common intermediate, δTDP‐4‐keto, 6‐deoxygiucose. ORF5 encodes a thioesterase similar to one encoded in the erythromycin gene cluster of Saccharopolyspora erythraea.