bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel chromatin‐forming histone H1 homologue is encoded by a dispensable and growth‐regulated gene in Bordetella pertussis
Authors: Scarlato Vincenzo , Aricó Beatrice , Goyard Sophie , Ricci Stefano , Manetti Riccardo , Prugnola Anna , Manetti Roberto , Polverino‐De‐Laureto Patrizia , Ullmann Agnes , Rappuoli Rino 
Published: October 2006

SummaryWe report the Identification of a protein homologous to a histone H1 in Bordetella pertussis. The B. pertussis histone homologue, BpH1, varies in size in different strains from 182 to 206 amino acids. The variability of the size of the protein is due to gene variability by insertion or deletion of DNA modules. Insertion of a kanamycin cassette into the bpH1 gene generates a BpH1 null mutant with phenotypic properties and growth rate similar to those of the wild‐type strain, showing that this gene is dispensable. In vitro, the BpH1 protein prevents chromosomal DNA degradation from DNase I and constrains supercoiled DNA. Transcription of the bpH1 gene is activated during exponential growth of the bacteria, whereas It is repressed during the stationary phase of growth, It is proposed that BpH1 plays a role in chromatin formation and condensation during DNA replication and that repression of transcription depends upon a reduced rate of DNA replication.
Action of receiver and activator modules of UhpA in transcriptional control of the Escherichia coli sugar phosphate transport system
Authors: Webber Carol A. , Kadner Robert J. 
Published: October 2006

SummaryInduction of the sugar‐phosphate transport system in Escherichia coli by external glucose‐6‐phosphate is regulated by the UhpABC regulatory proteins. UhpA protein is required for uhpT transcription and is related to response regulators of two‐component regulatory systems. UhpA and its homologues appear to be composed of two modules: the receiver module which contains the putative site of phosphorylation, and the activation module whose predicted helix‐turn‐helix motif is related to that present in many transcription activators. The roles of the two modules were examined by analysis of the regulatory consequences of uhpA deletion mutations generated by in vitro manipulations and missense mutations selected for independence from the requirement for UhpB kinase activity. Deletion of even seven amino acids from the C‐terminus resulted in complete loss of transcription activation at the uhpT promoter. Overexpression of all C‐terminal truncations that left intact the receiver module (residues 1–120) exhibited strong dominant‐negative interference with a chromosomal uhpA+ allele. The genetic requirements for interference indicated that the overexpressed receiver module competed with intact UhpA for phosphate residues carried on UhpB. The site of phosphorylation of UhpA is not necessary for uhp activation by over‐expressed UhpA but is necessary for UhpA action at normal levels of UhpA or for interference by the truncated species.
Molecular cloning, expression in Streptomyces livdans, and analysis of a gene cluster from Arthrobacter simplex encoding 3‐ketosteroid‐Δ1‐dehydrogenase, 3‐ketosteroid‐Δ5‐isomerase and a hypothetical regulatory protein
Authors: Molnár István , Choi Kwang‐Pil , Yamashita Mitsuo , Murooka Yoshikatsu 
Published: October 2006

SummaryThe Arthrobacter simplex gene coding for 3‐ketosteroid‐Δ1‐dehydrogenase, a key enzyme in the degradation of the steroid nucleus, was cloned in Streptomyces lividans, Nucleotide sequence analysis revealed that the gene for 3‐ketosteroid‐Δ1‐dehydrogenase (ksdD) is clustered with at least two more genes possibly involved in steroid metabolism. Upstream of ksdD, we found a gene, ksdR, encoding a hypothetical regulatory protein that shows homologies to KdgR, the negative regulator of pectin biodegradation in Erwinia, and GylR, the activator for glycerol metabolism in Steptomyces. A helix‐turn‐helix DNA‐binding domain can be predicted at similar positions near the N‐terminal of KsdR, KdgR and GylR. ksdl adjoining downstream to ksdD codes for a protein that has strong similarities to 3‐ketosteroid‐Δ5‐isomerases. The highly conserved Tyr and Asp residues are present in the active‐centre motif of the enzyme. The translated ksdD gene product was found to be similar to the 3‐ketosteroid‐Δ1‐dehydrogenase of Pseudomonas testosteroni and to the fumarate reductase of Shewanella putrefaciens. A region highly conserved between the two steroid dehydrogenases can be aligned to the active‐centre motif of the fumarate reductase. S. lividans strains carrying the ksdD gene overexpressed 3‐ketosteroid‐Δ1‐dehydrogenase. The expression of 3‐ketosteroid‐Δ5‐isomerase, however, was barely detectable in recombinant S. lividans strains carrying the ksdl gene, or in the parental Arthrobacter strain.
Small clusters of divergent amino acids surrounding the effector domain mediate the varied phenotypes of EF‐G and LepA expression
Authors: Yaskowiak Edward S. , March Paul E. 
Published: October 2006

SummaryElongation factors G, Tu, and related proteins (including LepA) form a distinct subgroup within the GTPase superfamily. This observation is based primarily upon amino acid comparisons of the effector region (G2) of the GTP‐binding domain. To examine the functional importance of the highly conserved elongation factor G2 domain a series of chimeric proteins were constructed between Escherichia coli EF‐G and Micrococcus luteus EF‐G, and between E. coli EF‐G and LepA (a protein of unknown function). The M. luteus EF‐G/E. coli EF‐G hybrid, M. luteus EF‐G, and E. coli EF‐G efficiently complemented EF‐G function in an E. coli strain (PEM101) harbouring a temperature‐sensitive mutation in fusA (the gene encoding EF‐G). A comparison of the amino acid sequences of the M. luteus EF‐G and E. coli EF‐G indicated that groups of divergent amino acid residues (amino acids 1–9 and 72–80) were not important for function. LepA and LepA/EF‐G chimeric proteins were tested for the ability to complement EF‐G function in vivo, for cross‐linking to 8‐azido‐[γ‐32]‐GTP in vitro and for fusidic acid‐dependent co‐sedimentation with 70S ribosomes. With one exception, all chimeras could be readily cross‐linked to azido‐GTP in an EF‐G‐like manner, indicating that hybrid protein construction did not generally result in improperly folded GTP‐binding domains. However, the inability of such chimeras to complement EF‐G function in vivo indicates that the effector domains are not functionally interchangeable. All LepA/EF‐G chimeric proteins were severely defective in fusidic acid‐dependent complex formation with 70S ribosomes. A comparison of the amino acid sequences of all three proteins suggests that residues 30–33, 43–48, and 63–66 of E. coli EF‐G are important for EF‐G specific ribosome‐associated function.
Developmentally regulated expression of a Giardia lamblia cyst wall protein gene
Authors: Mowatt Michael R. , Luján Hugo D. , Cotten David B. , Bowers Blair , Yee Janet , Nash Theodore E. , Stibbs Henry H. 
Published: October 2006

SummaryThe protozoan Giardia lamblia is an obligate parasite of the mammalian small intestine. We studied the expression of a gene that encodes a protein component of the cyst wall, a complex structure assembled during the differentiation of trophozoites to cysts and which is critical to survival of the parasite outside its mammalian host. Transcripts from the cyst wall protein gene increase more than 100‐fold during encystation, reaching a maximum between 5 and 24 hours after induction. Cyst wall protein expression also increases dramatically during encystation, and, prior to its incorporation into the nascent cyst wall, the protein is contained within the encystation‐specific vesicles of encysting trophozoites. The sequence of the cloned gene predicts an acidic, leucine‐rich polypeptide of Mr, 26000 that contains 5.3 tandemly arranged copies of a degenerate 24‐amino‐acid repeat. A hydrophobic amino‐terminal peptide probably serves as the initial signal that targets this protein to a secretory pathway involving vesicular localization during encystation and, ultimately, secretion to form the cyst wall.
The positively acting amdA gene of Aspergillus nidulans encodes a protein with two C2H2 zinc‐finger motifs
Authors: Lints Robyn , Davis Meryl A. , Hynes Michael J. 
Published: October 2006

SummarySemi‐dominant mutations in the amdA gene iead to elevated expression of the gene encoding acetamidase, amdS. These mutations also cause constitutive expression of the acetate‐inducible gene, aciA. In the amdS 5′ regulatory region, two cis‐acting mutations, amd166 anti amd1666, have been isolated which specifically affect amdA activation of amdS. These mutations are a duplication and a triplication of an 18bp GA‐rich sequence, thought to define the amdA site of action within the amdS promoter region. Similar GA‐rich sequences have also been found in the 5′ region of aciA. This paper describes the cloning and initial functional characterization of the amdA gene and two of its mutant alleles. The wild‐type amdA gene has been cloned by a chromosome walk from genes gatA and alcC on linkage group VII and localized by complementation of an amdA loss‐of‐function mutation. Transcriptional analysis reveals that the gene is expressed constitutively at low levels under growth conditions which affect expression of amdS and aciA. The gene is predicted to encode an 880‐amino‐acid protein which contains two C2H2 zinc fingers, a nuclear localization sequence and two transcriptional activation domains. The amdA7 semi‐dominant gain‐of‐function mutation results in a glycine to aspartate substitution which would increase the acidity of one of these regions. Analysis of in vitro generated mutations in the 5′ region of amdS using an amdS::lacZ reporter has been used to localize the site of action of AmdA. The C2H2 zinc‐finger motifs identified in the protein are similar to those found in the carbon catabolite repressor protein, CreA, which also regulates amdS and recognizes sequences which overlap with the proposed site of action for AmdA.
The Escherichia coli DnaK chaperone machine and bacteriophage Mu iate transcription
Authors: Sand Olivier , Desmet Lucie , Toussaint Ariane , Pato Martin 
Published: October 2006

SummaryBacteriophage Mu does not grow on temperature‐sensitive E. coli dnaK mutants at elevated temperatures because of a defect in late transcription. As the Mu‐encoded C protein is required for activation of transcription from the phage late promoters, we attempted to determine if DnaK and its accessory proteins DnaJ and GrpE are required for synthesis of C protein or at a later step. We found that the chaperones act in Mu late transcription beyond C‐protein synthesis, and that C‐protein stability is decreased in the mutant hosts. This suggests that the DnaK chaperone machine may be required for the proper folding and/or multi‐merization of C protein.
Mobile gene cassettes and integrons: capture and spread of genes by site‐specific recombination
Authors: Hall Ruth M. , Collis Christina M. 
Published: October 2006

SummaryAn integron is a genetic unit that includes the determinants of the components of a site‐specific recombination system capable of capturing and mobilizing genes that are contained in mobile elements called gene cassettes. An integron also provides a promoter for expression of the cassette genes, and integrons thus act both as natural cloning systems and as expression vectors. The essential components of an integron are an int gene encoding a site‐specific recombinase belonging to the integrase family, an adjacent site, attl, that is recognized by the integrase and is the receptor site for the cassettes, and a promoter suitably oriented for expression of the cassette‐encoded genes. The cassettes are mobile elements that include a gene (most commonly an antibiotic‐resistance gene) and an integrase‐specific recombination site that is a member of a family of sites known as 59‐base elements. Cassettes can exist either free in a circularized form or integrated at the attl site, and only when integrated is a cassette formally part of an integron. A single site‐specific recombination event involving the integron‐associated attl site and a cassette‐associated 59‐base element leads to insertion of a free circular cassette into a recipient integron. Multiple cassette insertions can occur, and integrons containing several cassettes have been found in the wild. The integrase also catalyses excisive recombination events that can lead to loss of cassettes from an integron and generate free circular cassettes. Due to their ability to acquire new genes, integrons have a clear role in the evolution of the genomes of the plasmids and transposons that contain them. However, a more general role in evolution is also likely. Events involving recombination between a specific 59‐base‐element site and a nonspecific secondary site have recently been shown to occur. Such events should lead either to the insertion of cassettes at non‐specific sites or to the formation of stable cointegrates between different plasmid molecules, and a cassette situated outside the integron context has recently been identified.
The twisted ‘life’ of DNA in the cell: bacterial topoisomerases
Authors: Luttinger Amy 
Published: October 2006

SummaryDNA topoisomerases are essential to the cell for the regulation of DNA supercoiling levels and for chromosome decatenation. The proposed mechanisms for these reactions are essentially the same, except that a change in supercoiling is due to an intramolecular event, while decatenation requires an intermolecular event. The characterized bacterial topoisomerases appear capable of both types of reaction in vitro. Four DNA topoisomerases have been identified in Escherichia coli. Topoisomerase I, gyrase, and topoisomerase IV normally appear to have distinct essential functions within the cell, Gyrase and topoisomerase I are responsible for the regulation of DNA supercoiling. Both gyrase and topoisomerase IV are necessary for chromosomal decatenation. Multiple topoisomerases with distinct functions may give the cell more precise control over DNA topology by allowing tighter regulation of the principal enzymatic activities of these different proteins.
Chlamydial envelope components and pathogen‐host cell interactions
Authors: Raulston Jane E. 
Published: October 2006

SummaryFew bacterial pathogens are as widespread in nature or as capable of eliciting such a diversity of disease syndromes as are the chlamydiae. As obligate intra‐cellular organisms, they pose a special research challenge in defining the molecular components and mechanisms for productive growth within host cells and the overall progress of infection throughout host tissue. Although a comprehensive view of chlamydial envelope composition and respective functions in pathogenesis is far from complete, ongoing investigations continue to expose new and intriguing avenues for exploration.
The enterotoxin gene (cpe) of Clostridium perfringens can be chromosomal or plasmid‐borne
Authors: Cornillot Emmanuel , Saint‐Joanis Brigitte , Daube Georges , Katayama Sei‐ichi , Granum Per Einar , Canard Bruno , Cole Stewart T. 
Published: October 2006

SummaryThe location of the cpe gene, encoding the enterotoxin responsible for food poisoning in humans, has been studied in a series of enterotoxigenic Ciostridium perfringens strains by means of pulsed field gel electrophoresis of genomic DNA. The cpe gene was found at the same chromosomal locus in strains associated with food poisoning in humans and was shown to be linked to a repetitive sequence, the Hin dlll repeat, and an open reading frame, ORF3, that may be part of an insertion sequence. In contrast, when the strains originated from domesticated livestock cpe was located on a large episome where it was often close to a copy of the transposable element IS 1151. In these cases, the Hin dlll repeat was not linked to the cpe gene although this was generally preceded by ORF3.
Protective antigen‐binding domain of anthrax lethal factor mediates translocation of a heterologous protein fused to its amino‐ or carboxy‐terminus
Authors: Milne Jill C. , Blanket Steven R. , Hanna Philip C. , Collier R. John 
Published: October 2006

SummaryThe edema factor (EF) and lethal factor (LF) components of anthrax toxin require anthrax protective antigen (PA) for binding and entry into mammalian cells. After internalization by receptor‐mediated endocytosis, PA facilitates the translocation of EF and LF across the membrane of an acidic intracellular compartment. To characterize the translocation process, we generated chimeric proteins composed of the PA recognition domain of LF (LFN; residues 1–255) fused to either the amino‐terminus or the carboxy‐terminus of the catalytic chain of diphtheria toxin (DTA). The purified fusion proteins retained ADP‐ribosyltransferase activity and reacted with anti‐sera against LF and diphtheria toxin. Both fusion proteins strongly inhibited protein synthesis in CHO‐K1 cells in the presence of PA, but not in its absence, and they showed similar levels of activity. This activity could be inhibited by adding LF or the LFN fragment (which blocked the interaction of the fusion proteins with PA), by adding inhibitors of endo‐some acidification known to block entry of EF and LF into cells, or by introducing mutations that attenuated the ADP‐ribosylation activity of the DTA moiety. The results demonstrate that LFN fused to either the amino‐terminus or the carboxy‐terminus of a heterologous protein retains its ability to complement PA in mediating translocation of the protein to the cytoplasm. Besides its importance in understanding translocation, this finding provides the basis for constructing a translocation vector that mediates entry of a variety of heterologous proteins, which may require a free amino‐ or carboxy‐terminus for biological activity, into the cytoplasm of mammalian cells.
Phosphorylation and functional analysis of PilA, a protein involved in the transcriptional regulation of the pilin gene in Neisseria gonorrhoeae
Authors: Taha Muhamed‐Kheir , Giorgini Dario 
Published: October 2006

SummaryThe transcriptional regulation of the pilE gene, coding for the pilin in Neisseria gonorrhoeae, by PilA/PilB proteins is quite complex. Sequence analysis of PilA suggested that it has multiple domains. PilA appears to have in its N‐terminal half a DNA‐binding site followed by a region showing sequence similarity with other bacterial transcriptional regulators. In its C‐terminal half, PilA has extensive homology with the 54kDa protein of the eukaryotic signal‐recognition particle which is involved in protein secretion. A transcriptional fusion between the promoter of pilE and the lacZ gene was constructed and integrated into the gonococcal chromosome. We show that transcription of the pilE‐lacZ fusion is affected in pHA mutants in the absence of any possible interference with pilin secretion. Moreover, pilE transcription depends on a 24/‐12‐type promoter which could be a member of a family of promoters recognized by the alternative Sigma subunit, RpoN, of the RNA polymerase. We also show that PilA binds specifically to the promoter region of pilE and that it is phosphorylated in a manner dependent on acidic residues Glu‐59, Asp‐149 and Asp‐186. The functional organization of PilA suggests that it may be an unusual transcriptional regulator different from other RpoN‐dependent activators.
Localization of the start sites of lagging‐strand replication of rolling‐circle plasmids from Gram‐positive bacteria
Authors: Dempsey Laurie A. , Zhao Adam C. , Khan Saleem A. 
Published: October 2006

SummaryA number of small, multicopy plasmids from Gram‐positive bacteria replicate by an asymmetric rolling‐circle mechanism. Previous studies with several of these plasmids have identified a palindromic sequence, SSOA, that acts as the single‐strand origin (SSO) for the replication of the lagging‐strand DNA. Although not all the SSOA sequences share ONA sequence homology, they are structurally very similar. We have used an in vitro system to study the lagging‐strand replication of several plasmids from Gram‐positive bacteria using the SSOA sequences of pT181, pE194 and pSN2 as representative of three different groups of Staphylococcus aureus plasmids. In addition, we have investigated the lagging‐strand replication of the pUB110 plasmid that contains an alternative single‐strand origin, ssou. Our results confirm that RNA polymerase is involved in lagging‐strand synthesis from both SSOA and ssou‐type lagging‐strand origins. Interestingly, while initiation of lagging‐strand DNA synthesis of pUB110 occurred predominantly at a single position within ssou, replication of pT181, pSN2 and pE194 plasmids initiated at multiple positions from SSOA.
A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon
Authors: Slack Frank J. , Serror Pascale , Joyce Elizabeth , Sonenshein Abraham L. 
Published: October 2006

SummaryAn insertion mutation was isolated that resulted in derepressed expression of the Bacillus subtilis dipeptide transport operon (dpp) during the exponential growth phase in rich medium. DNA flanking the site of insertion was found to encode an operon (codVWXY) of four potential open reading frames (ORFs). The deduced product of the codV ORF is similar to members of the λ Int family; CodW and CodX are homologous to HsIV and HsIU, two putative heat‐shock proteins from Escherichia coli, and to LapC and LapA, two gene products of unknown function from Pasteurella haemolytica. CodX also shares homology with a family of ATPases, including CIpX, a regulatory subunit of the E. coli ClpP protease. CodY does not have any homologues in the databases. The insertion mutation and all previously isolated spontaneous cod mutations were found to map In codY. In‐frame deletion mutations in each of the other cod genes revealed that only codY is required for repression of dpp in nutrient‐rich medium. The cody mutations partially relieved amino acid repression of the histidine utilization (hut) operon but had no effect on regulation of certain other early stationary phase‐induced genes, such as spoVG and gsiA.
The Pseudomonas aeruginosa pilK gene encodes a chemotactic methyltransferase (CheR) homologue that is translationally regulated
Authors: Darzins Aldis 
Published: October 2006

SummaryA new locus, designated pilK, located immediately adjacent to the previously described Pseudomonas aeruginosa pilG–J gene cluster, has been identified. Sequence analysis of a 1.3 kb region revealed the presence of a single open reading frame of 291 amino acid residues (Mr, 33 338) that contained significant homology to the chemotactic methyltransferase proteins of Escherichia coli. Bacillus subtilis and the gliding bacterium Myxococcus xanthus. The 60 bp pilJ–pilK intergenic region was devoid of promoter consensus sequences, suggesting that pilj and pilK are contained within the same transcriptional unit. The intergenic region did contain, however, a large, highly GC‐rich, inverted repeat that prevented PilK production in expression studies. To investigate the regulatory role of these sequences, pilK‐lacZ gene fusions, as well as derivatives containing sequence alterations in the potential stem‐loop region, were constructed and analysed in E. coli and P. aeruginosa. Modification of the inverted repeat region in pilK‐lacZ protein fusion constructs resulted in as much as a 24'fold increase in β‐galactosidase activity, whereas similar modifications in pilK‐lacZ transcriptional fusions had only a marginal effect on β‐galactosidase levels. These results indicated that PilK production may be largely regulated at the level of translation. In stark contrast to pilG‐J mutants, which are dramatically impaired in pilus production and/or function, a PAO1 pilK deletion mutant was indistinguishable from the wild type. In addition, complementation studies suggested that the PilK and E. coli CheR proteins are not functionally interchangeable.