bluuebunny/crossref_metadata_2025_split huggingface dataset:
From acids to osmZ: multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli
Authors: Pratt Leslie A. , Hsing Weihong , Gibson Katherine E. , Silhavy Thomas J. 
Published: October 2006

SummaryIn Escherichia coli, levels of the two major outer membrane porin proteins, OmpF and OmpC, are regulated in response to a variety of environmental parameters, and numerous factors have been shown to influence porin synthesis. EnvZ and OmpR control porin‐gene transcription in response to osmolarity, and the anti‐sense RNA, MicF, influences ompF translation. In contrast to these characterized factors, some of the components reported to influence porin expression have only modest effects and/or act indirectly. For others, potential regulatory roles, although intriguing, remain elusive. Here we review many of the components that have been reported to influence porin expression, address the potential regulatory nature of these components, and discuss how they may contribute to a regulatory network controlling porin synthesis.
Assembly of human contact phase proteins and release of bradykinin at the surface of curli‐expressing Escherichia coli
Authors: Ben Nasr Abdelhakim , Olsén Arne , Sjöbring Ulf , Müller‐Esterl Werner , Björck Lars 
Published: October 2006

Summary Previous work has demonstrated that most strains of the human pathogen Streptococcus pyogenes bind kininogens through M protein, a fibrous surface protein and virulence determinant. Here we find that strains of several other pathogenic bacterial species, both Gram‐positive and Gram‐negative, isolated from patients with sepsis, also bind kininogens, especially H‐kininogen (HK). The most pronounced interaction was seen between HK and Escherichia coli. Among clinical isolates of E. coli, the majority of the entero‐haemorrhagic, enterotoxigenic, and sepsis strains, but none of the enteroinvasive and enteropathogenic strains, bound HK. Binding of HK to E. coli correlated with the expression of curli, another fibrous bacterial surface protein, and the binding of HK to purified curli was specific, saturable, and of high affinity; Ka = 9 107M‐1. Other contact phase proteins such as factor XI, factor XII, and prekallikrein bound to curliated E. coli, but not to an isogenic curli‐deficient mutant strain, suggesting that contact phase activation may occur at the surface of curliated bacteria. Kininogens are also precursor molecules of the vasoactive kinins. When incubated with human plasma, curli‐expressing bacteria absorbed HK. Addition of purified plasma kallikrein to the HK‐loaded bacteria resulted in a rapid and efficient release of bradykinin from surface‐bound HK. The assembly of contact phase factors at the surface of pathogenic bacteria and the release of the potent proinflammatory and vasoactive peptide bradykinin, should have a major impact on the host‐microbe relationship and may contribute to bacterial pathogencity and virulence.
Escherichia coli strains in which chromosome replication is controlled by a P1 or F replicon integrated into oriC
Authors: Eliasson Åsa , Nordström Kurt , Bernander Rolf 
Published: October 2006

SummaryWe report the construction of intP1 and intFs strains, in which the basic replicon from either plasmid P1 or plasmid F (oriS) has been integrated in both orientations into the origin of replication, oriC, of the Escherichia coli chromosome. In these strains, oriC is no longer functional and chromosome‐replication is instead controlled by the integrated plasmid replicon. The strains were viable, showing that the deviation from normal chromosome‐replication control was not large enough to prohibit cell survival. The strains showed a broader cell‐size distribution than a wild‐type strain and were more filamentous in rich than in minimal media, although cells of wild‐type size were also present. Cells which contained aberrantly shaped or aberrantly distributed nucleoids were also observed. Marker‐frequency analysis indicated that chromosome replication was predominantly bidirectional in both intFs strains. In the intP1 strains, the degree of bidirectionality depended upon the orientation of the integrated replicon.
Circadian expression of genes involved in the purine biosynthetic pathway of the cyanobacterium Synechococcus sp. strain PCC 7942
Authors: Liu Yi , Tsinoremas Nicholas F. , Golden Susan S. , Kondo Takao , Johnson Carl Hirschie 
Published: October 2006

SummaryExtensive circadian (daily) control over gene expression in the cyanobacterium Synechococcus sp. strain PCC 7942 is programmed into at least two differentially phased groups. The transcriptional activity of the smaller group of genes is maximal at about dawn and minimal at about dusk. We identified one of the genes belonging to this latter group as purF, which encodes the key regulatory enzyme in the de novo purine synthetic pathway, glutamine PRPP amidotransferase (also known as amidophosphoribosyltransferase). Its expression pattern as a function of circadian time was confirmed by both luminescence from a purF:: luxAB reporter strain and the abundance of purF mRNA. By fusing sequences upstream of the purF coding region to promoterless luxAB genes, we identified a limited upstream region, which potentially regulates purF circadian expression patterns in vivo. We also identified the purL gene immediately upstream of purF. The purL gene encodes FGAM synthetase, the fourth enzyme in the purine nucleotide biosynthesis pathway. Although these genes are expressed as part of a larger operon in other bacteria, reporter gene fusions revealed that purF and purL are transcribed independently in Synechococcus and that they are expressed at different phases of the circadian cycle. This differential expression pattern may be related to the oxygen sensitivity of amidophosphoribosyltransferase.
RbfA, a 30S ribosomal binding factor, is a cold‐shock protein whose absence triggers the cold‐shock response
Authors: Jones Pamela G. , Inouye Masayori 
Published: October 2006

Summary The cold‐shock response, characterized by a specific pattern of gene expression, is induced upon a downshift in temperature and in the presence of inhibitors of ribosomal function. Here, we demonstrate that RbfA of Escherichia coli, considered to be involved in ribosomal maturation and/or initiation of translation, is a cold‐shock protein. Shifting the rbfA mutant to a lower temperature resulted in a constitutive induction of the cold‐shock response accompanied by slower growth at low temperatures, while shifting the rbfA mutant that overproduces wild‐type RbfA resulted in an increase in total protein synthesis accompanied by faster growth adaptation to the lower temperature. Furthermore, the cold‐shock response was also constitutively induced in a cold‐sensitive 16S rRNA mutant at low temperatures. Accompanying the transient induction of the cold‐shock response, we also report that shifting E. coli from 37°C to 15°C resulted in a temporary inhibition of initiation of translation, as evidenced by the transient decrease in polysomes accompanied by the transient increase in 70S monosomes. The accumulative data indicate that the inducing signal for the cold‐shock response is the increase in the level of cold‐unadapted non‐translatable ribo‐somes which are converted to cold‐adapted translatable ribosomes by the association of cold‐shock proteins such as RbfA. Therefore, the expression of the cold‐shock response, and thus cellular adaptation to low temperature, is regulated at the level of translation. The data also indicate that cold‐shock proteins can be translated by ribosomes under conditions that are not translatable for most mRNAs.
The vacuolating cytotoxin of Helicobacter pylori
Authors: Cover Timothy L. 
Published: October 2006

Summary Helicobacter pylori, the causative agent of chronic superficial gastritis and duodenal ulcer disease in humans, produces a unique cytotoxin (VacA) that induces cytoplasmic vacuolation in eukaryotic cells. The structural organization and processing of the vacuolating cytotoxin are characteristic of a family of proteins exemplified by Neisseria gonorrhoeae IgA protease. Although only 50% of H. pylori isolates produce detectable cytotoxin activity in vitro, vacA homologues are present in virtually all isolates. Several families of vacA alleles have been identified, and there is a strong correlation between presence of specific vacA genotypes, cytotoxin activity, and peptic ulceration. Experiments in a mouse model of H. pylori‐induced gastric damage indicate that the cytotoxin plays an important role in inducing gastric epithelial necrosis.
EspA, a protein secreted by enteropathogenic Escherichia coli, is required to induce signals in epithelial cells
Authors: Kenny Brendan , Lai Li‐Ching , Finlay B. Brett , Donnenberg Michael S. 
Published: October 2006

SummaryEnteropathogenic Escherichia coli (EPEC) is a leading cause of infant diarrhoea. EPEC mediates several effects on host epithelial cells, including activation of signal‐transduction pathways, cytoskeletal rearrangement along with pedestal and attachingleffacing lesion formation. It has been previously shown that the EPEC eaeB (espB) gene encodes a secreted protein required for signal transduction and adherence, while eaeA encodes intimin, an EPEC membrane protein that mediates intimate adherence and contributes to focusing of cytoskeletal proteins beneath bacteria. DNA‐sequence analysis of a region between eaeA and eaeB identified a predicted open reading frame (espA) that matched the amino‐terminal sequence of a 25 kDa EPEC secreted protein. A mutant with a non‐polar insertion in espA does not secrete this protein, activate epithelial cell signal transduction or cause cytoskeletal rearrangement. These phenotypes were complemented by a cloned espA gene. The espA mutant is also defective for invasion. It is concluded that espA encodes an EPEC secreted protein that is necessary for activating epithelial signal transduction, intimate contact, and formation of attaching and effacing lesions, processes which are central to pathogenesis.
A cluster of fourteen genes from enteropathogenic Escherichia coli is sufficient for the biogenesis of a type IV pilus
Authors: Stone Kelly D. , Zhang Hong‐Zhong , Carlson Lisa K. , Donnenberg Michael S. 
Published: October 2006

SummaryEnteropathogenic Escherichia coli (EPEC) adhere to epithelial cells in microcolonies, a pattern termed localized adherence (LA). LA is dependent upon the presence of 50–70MDa plasmids, termed EPEC adherence factor (EAF) plasmids. Expression of an EAF plasm id‐encoded type IV fimbria, the bundle‐forming pilus (BFP), is associated with the LA phenotype. TnphoA insertions in bfpA, the gene encoding the major structural subunit of the BFP, abolish LA. While bfpA::TnphoA mutants cannot be complemented for LA by plasmids carrying the bfpA gene alone in trans, this work shows that they can be complemented by plasmids carrying the bfpA gene, as well as approximately 10kb of downstream sequence, suggesting that such mutations have polar effects on downstream genes. The identification and characterization of a cluster of 13 genes immediately downstream of bfpA are described. The introduction into a laboratory Escherichia coli strain of a plasmid containing these 14 bfp gene cluster genes, along with pJPN14, a plasmid containing another fragment derived from the EAF plasmid, confers LA ability and BFP biogenesis. However, when a mutation is introduced into the last gene of the bfp cluster, neither LA nor BFP biogenesis is conferred. This work also provides evidence to show that the fragment cloned in pJPN14 encodes a factor(s) which results in increased levels of the pilin protein. Finally, it is shown that expression of the 14 genes in the bfp cluster from an IPTG‐inducible promoter, in the absence of pJPN14, is sufficient to reconstitute BFP biogenesis in a laboratory E. cob strain, but is insufficient for LA. This is the first report demonstrating the reconstitution of a type IV pilus in a laboratory E. coli strain with a defined set of genes. The 8FP system should prove to be a useful model for studying the molecular mechanisms of type IV pilus biogenesis.
Bacillus subtilis operon under the dual control of the general stress transcription factor σB and the sporulation transcription factor σH
Authors: Varón Débora , Brody Margaret S. , Price Chester W. 
Published: October 2006

SummaryThe σB transcription factor of Bacillus subtilis is activated in response to a variety of environmental stresses, including those imposed by entry into the stationary‐growth phase, and by heat, salt or ethanol challenge to logarithmically growing cells. Although σB is thought to control a general stress regulon, the range of cellular functions it directs remains largely unknown. Our approach to understand the physiological role of σB is to characterize genes that require this factor for all or part of their expression, i.e. the csb genes. In this study, we report that the transposon insertion csb40::Tn917lac identifies an operon with three open reading frames, the second of which resembles plant proteins induced by desiccation stress. Primer‐extension and operon‐fusion experiments showed that the csb40 operon has a σB‐dependent promoter which is strongly induced by the addition of salt to logarithmically growing cells. The csb40 operon also has a second, σH‐dependent promoter that is unaffected by salt addition. These results provide support for the hypothesis that σB controls a general stress regulon, and indicate that the σB and σH regulons partly overlap. We suggest that in addition to its acknowledged role in the sporulation process, σH is also involved in controlling a subclass of genes that are broadly involved in a general stress response.
Differential regulation of the virulence genes of Listeria monocytogenes by the transcriptional activator PrfA
Authors: Bohne Jutta , Kestler Hubert , Uebele Corinna , Sokolovic Zeljka , Goebel Werner 
Published: October 2006

SummaryThe two Listeria monocytogenes strains EGD and NCTC 7973 display a different regulation pattern of their PrfA‐dependent genes. All PrfA‐dependent genes from L. monocytogenes NCTC 7973 are much more efficiently transcribed in brain‐heart infusion medium than those from strain EGD. Transcription of these genes in EGD is, however, induced after shift into Minimal Essential Medium (MEM) to a level that is comparable to that of strain NCTC 7973. Expression of the internalin gene (inIA) is also influenced by PrfA, but only one (P2) out of three mapped promoters is strictly dependent on PrfA. In contrast to the other PrfA‐regulated genes, transcription of inIA even from the P2 promoter is reduced in both strains after shift to MEM. The prfA deletion mutant SLCC 53 complemented with multiple copies of prfA synthesizes large amounts of monocistronic prfA transcript, but there is no concomitant increase in the transcripts of the PrfA‐dependent genes. However, upon a shift into MEM, transcription of the PrfA‐dependent genes (with the exception of the inIA gene) is highly induced even in the absence of de novo protein synthesis. The PrfA proteins of the two studied L. monocytogenes strains differ in their ability to activate PrfA‐dependent genes. This difference is probably the result of amino acid exchange(s) in the C‐terminal part of these proteins. Strain EGD supplemented with multiple copies of prfA‐7973 shows a similar regulation of the PrfA‐dependent genes as strain NCTC 7973, whereas multiple copies of prfA‐EGD introduced into strain EGD hardly change the rate of transcription of the PrfA‐dependent genes. Our data thus suggest that PrfA‐mediated gene expression depends not only on the amount of the PrfA protein and the ‘quality’ of the putative PrfA‐binding sites, but also on the ‘quality’ of the PrfA protein which seems to be influenced by its amino acid composition and by environmental parameters.
Localization of OccR‐activated and TraR‐activated promoters that express two ABC‐type permeases and the traR gene of Ti plasmid pTiR10
Authors: Fuqua Clay , Winans Stephen C. 
Published: October 2006

Summary Conjugation of Agrobacterium tumefaciens wide‐host‐range octopine‐type Ti plasmids is regulated by the LuxR‐type transcriptional activator TraR in conjunction with an acylated homoserine lactone designated AAI. Expression of traR in octopine‐type Ti plasmids is stimulated by OccR in response to octopine, an opine released from crown gall tumours, and is also positively autoregulated by TraR and AAI. Genetic and physical mapping of these promoters indicates that the OccR‐activated promoter lies 14.5 kb upstream of traR, while the TraR‐activated promoter lies 6kb upstream. The upstream portion of the 14.5 kb operon contains seven previously characterized genes that direct the uptake and catabolism of octopine. The TraR‐activated promoter lies just downstream from the octopine catabolic genes, and transcribes six genes in addition to traR, including five genes (ophABCDE) that show strong homology to oligopeptide permeases of Salmonella typhimurium and Bacillus subtilis. Several TraR‐regulated promoters overlap with 18bp inverted repeats called tra boxes. In contrast, the traR autoregulatory promoter is not associated with a consensus tra box.
Capsule phase variation in Neisseria meningitidis serogroup B by slipped‐strand mispairing in the polysialyltransferase gene (siaD): correlation with bacterial invasion and the outbreak of meningococcal disease
Authors: Hammerschmidt Sven , Müller Astrid , Sillmann Hanna , Miihlenhoff Martina , Borrow Raymond , Fox Andrew , van Putten Jos , Zollinger Wendell D. , Gerardy‐Schahn Rita , Frosch Matthias 
Published: October 2006

SummaryA mechanism of capsular polysaccharide phase variation in Neisseria meningitidis is described. Meningococcal cells of an encapsulated serogroup B strain were used in invasion assays. Only unencapsulated variants were found to enter epithelial cells. Analysis of one group of capsule‐deficient variants indicated that the capsular polysaccharide was re‐expressed at a frequency of 10−3. Measurement of enzymatic activities involved in the biosynthesis of the α‐2,8 polysialic acid capsule showed that polysialyltransferase (PST) activity was absent in these capsule‐negative variants. Nucleotide sequence analysis of siaD revealed an insertion or a deletion of one cytidine residue within a run of (dC)7 residues at position 89, resulting in a frameshift and premature termination of translation. We analysed unencapsulated isolates from carriers and encapsulated case isolates collected during an outbreak of meningococcal disease. Further paired blood‐culture isolates and unencapsulated nasopharyngeal isolates from patients with meningococcal meningitis were examined. In all unencapsulated strains analysed we found an insertion or deletion within the oligo‐(dC) stretch within siaD, resulting in a frameshift and loss of capsule formation. All encapsulated isolates, however, had seven dC residues at this position, indicating a correlation between capsule phase variation and bacterial invasion and the out‐break of meningococcal disease.
FIS is a regulator of metabolism in Escherichia coli
Authors: González‐Gil Gardenia , Bringmann Peter , Kahmann Regine 
Published: October 2006

SummaryThe Escherichia coli DNA‐binding protein FIS (factor for inversion stimulation) stimulates site‐specific recombination reactions catalysed by DNA invertases and is an activator of stable RNA synthesis. To address the question of whether FIS is involved in other cellular processes we have identified and sequenced proteins whose expression pattern is affected by FIS. This has led to the identification of several E. coli genes whose expression in vivo is either enhanced or repressed by FIS. All of these genes encode enzymes or transport proteins involved in the catabolism of sugars or nucleic acids, and their expression is also dependent on the cAMP‐CRP complex. In most cases studied the regulation by FIS is indirect and occurs through effects on the synthesis of the respective repressor proteins. We conclude that FIS is a transcriptional modulator involved in the regulation of metabolism in E. coli.
Preferential processing of the S1 subunit of pertussis toxin that is bound to eukaryotic cells
Authors: Finck‐Barbançon Viviane , Barbieri Joseph T. 
Published: October 2006

Summary Labelled [125l]‐pertussis toxin was prepared and used to measure the association of pertussis toxin (PT) to eukaryotic cells. PT was radioiodinated by the lactoperoxidase method which preferentially radioiodinated the S1 subunit. PT was radioiodinated at a high specific activity and possessed the same cytotoxicity as native PT as demonstrated by the ability to cluster Chinese hamster ovary (CHO) cells. Cell association of [125l]‐PT was not inhibited by excess non‐radiolabelled PT, which indicated that the initial interaction between PT and CHO cells involved a large number of low‐affinity receptors. At 37° C, the S1 within cell‐associated PT was preferentially processed to an S1 with a lower apparent molecular weight (termed S1p). This processing was inhibited by the addition of unlabelled PT, indicating that the processing event was saturable and specific. S1 processing occurred in CHO, Madin‐Darby canine kidney (MDCK) cells, and pig kidney (LLC‐PK1) cells. A pulse‐chase experiment showed that, at 37° C but not at 22° C, essentially all of the cell‐associated S1 was processed within 3 h of a chase. Reagents that were previously shown to inhibit the ability of PT to ADP‐ribosylate G1 proteins in intact CHO cells also inhibited the preferential processing of S1 within cell‐associated PT, in the order of efficiency: 22°C chloroquine nocodazole brefeldin A. This indicates that S1 processing requires an early endosomal function.
Identification and characterization of AlgZ, an AlgT‐dependent DNA‐binding protein required for Pseudomonas aeruginosa algD transcription
Authors: Baynham Patricia J. , Wozniak Daniel J. 
Published: October 2006

SummaryTranscriptional activation of the Pseudomonas aeruginosa algD gene results in high‐level synthesis of the capsular polysaccharide alginate, an important P. aeruginosa virulence factor expressed in cystic fibrosis (CF) patients with chronic pulmonary disease. In this study, electrophoretic mobility‐shift assays were used to identify a novel protein (AlgZ), which binds specifically to a sequence located 280 bp upstream of the algD promoter. While AlgZ‐binding activity did not require the response regulators AlgB or AlgR, expression of AlgZ was found to be absolutely dependent on the alternative sigma factor AlgT. Electrophoretic mobility‐shift assays and copper‐phenanthroline foot‐printing localized AlgZ binding to a 36 bp algD region, which includes several helical repeats. A collection of alginate‐producing (mucoid) and non‐mucoid P. aeruginosa strains, derived from CF patients, was characterized for AlgZ‐binding activity. In all cases, AlgZ binding to algD sequences was observed when extracts derived from mucoid P. aeruginosa CF isolates were examined. However, this binding activity was not present when extracts from non‐mucoid P. aeruginosa CF isolates were tested. Oligonucleotide mutagenesis was employed to create an algD allele with a 4 bp mutation in the predicted AlgZ‐binding site (algD38) and a heterologous substitution allele (algD40), in which the entire AlgZ‐binding site was replaced with a nonspecific DNA sequence of identical size. When the algD38 mutation was cloned into an algD‐cat transcriptional fusion, this resulted in a 28‐fold reduction in algD expression, whereas the algD40 mutation abolished algD transcription, indicating that AlgZ acts as an activator of algD transcription. These results support the hypothesis that activation of algD involves the formation of a high‐order looped structure allowing for multivalent contacts between AlgZ, AlgR and RNA polymerase containing the alternative sigma factor AlgT. Characterization of the molecular details of algD activation will provide insights into the control of other prokaryotic and eukaryotic promoters that utilize multiple activators.