bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overlaps and parallels in the regulation of intrinsic multiple‐antibiotic resistance in Escherichia coli
Authors: Miller Paul F. , Sulavik Mark C. 
Published: October 2006

SummaryChromosomally encoded systems present in a variety of bacteria appear to play a central role in determining the intrinsic level of resistance to many commonly used antibiotics. Work with the Gram‐negative bacterium Escherichia coli has shown that there is significant similarity at the amino acid sequence level among the structural components of these resistance systems as well as among their genetic regulators. This review describes two of the better‐studied regulatory systems, marRAB and soxRS, as well as two regulated multidrug‐efflux systems, encoded by emrAB and acrAB, and focuses on conserved themes in their primary structures and environmental stimuli. The observed resistance to clinically important antibiotics appears to reflect an overlap with broad‐ranged adaptive responses by free‐living bacteria to noxious plant materials in their natural environment.
Intracellular endosymbiotic bacteria of Camponotus species (carpenter ants): systematics, evolution and ultrastructural characterization
Authors: Schröder Doris , Deppisch Heike , Obermayer Malu , Krohne Georg , Stackebrandt Erko , Hölldobler Bert , Goebel Werner , Gross Roy 
Published: October 2006

Summary Intracellular endosymbiotic bacteria inherent to ants of the genus Camponotus were characterized. The bacteria were localized in bacteriocytes, which are specialized cells of both workers and queen ants; these cells are intercalated between epithelial cells of the midgut. The bacteriocytes show a different morphology from the normal epithelial cells and carry a large number of the rod‐shaped Gram‐negative bacteria free in the cytoplasm. The bacteria were never observed in the neighbouring epithelial cells, but they were found intracellularly in oocytes, strongly indicating a maternal transmission of the bacteria. The 16S DNA encoding rrs loci of the endosymbionts of four species of the genus Camponotus derived either from Germany (C. herculeanus and C. ligniperdus), North America (C. floridanus) or South America (C. rufipes) were cloned after polymerase chain reaction (PCR) amplification using oligonucleotides complementary to all so far known eubacterial rrs sequences. The DNA sequences of the rrs loci of the four endosymbionts were determined, and, using various genus‐ and species‐specific oligonucleotides derived from variable regions in the rrs sequences, the identity of the bacteria present in the bacteriocytes and the ovarian cells was confirmed by PCR and in situ hybridization techniques. Comparison of the 16S DNA sequences with the available database showed the endosymbiotic bacteria to be members of the γ‐subclass of Proteobacteria. They formed a distinct taxonomic group, a sister taxon of the taxons defined by the tsetse fly and aphid endosymbionts. Within the γ‐subclass, the cluster of the ant, tsetse fly and aphid endosymbionts are placed adjacent to the family of Enterobacteriaceae. The evolutionary tree of the ant endosymbionts reflects the systematic classification and geographical distribution of their host insects, indicating an early co‐evolution of the symbiotic partners and a vertical transmission of the bacteria.
The positions of the sigma‐factor genes, whiG and sigF, in the hierarchy controlling the development of spore chains in the aerial hyphae of Streptomyces coelicolor A3(2)
Authors: Kelemen Gabriella H. , Brown Gary L. , Kormanec Ján , Potúčkova Laura , Chater Keith F. , Buttner Mark J. 
Published: October 2006

Summary
whiG and sigF encode RNA polymerase sigma factors required for sporulation in the aerial hyphae of Streptomyces coelicolor. Their expression was analysed during colony development in wild‐type and sporulation‐defective whi mutant strains. Each gene was transcribed from a single promoter. Unexpectedly, whiG mRNA was present at all time points, including those taken prior to aerial mycelium formation; this suggests that whiG may be regulated post‐transcriptionally. Transcription of whiG did not depend upon any of the six known‘early’whi genes required for sporulation septum formation (whiA, B, G, H, /and J), placing it at the top of the hierarchy of whi loci. sigF expression appeared to be regulated at the level of transcription; sigF transcripts were detected transiently when sporulation septa were observed in the aerial hyphae. Transcription of sigF depended upon all six of the early whi genes, including whiG. The sigF promoter does not resemble the consensus sequence established for σWhiG‐dependent promoters and EnWhiG did not transcribe from the sigF promoter in vitro. Consequently, the genetic dependence of sigF upon whiG is very likely to be indirect. These results show that there is a hierarchical relationship between sigma factors required for Streptomyces sporulation and also that at least five other genes are involved in this transcriptional network.
Transcriptional activator of phage φ29 late promoter: mapping of residues involved in interaction with RNA polymerase and in DNA bending
Authors: Mencía Mario , Monsalve María , Salas Margarita , Rojo Fernando 
Published: October 2006

SummaryPhage φ29 regulatory protein p4 activates transcription from the late A3 promoter by stabilizing σA‐RNA polymerase at the promoter as a closed complex. Activation requires interaction between both proteins. Protein p4 bends the DNA upon binding. We have performed a detailed mutagenesis study of the carboxyl end of the protein, which is involved in both transcription activation and DNA bending. The results indicate that Arg‐120 is the most critical residue for activation, probably mediating the interaction with RNA polymerase. Several basic residues have been identified, including Arg‐120, that contribute to maintenance of the DNA bending, probably via electrostatic interactions with the DNA backbone. The degree or stability of the induced bend apparently relies on the additive contribution of all basic residues of the carboxyl end of the protein. Therefore, the activation and DNA bending surfaces overlap, and Arg‐120 should interact with both DNA and RNA polymerase. As we show that protein p4 is a dimer in solution, and is bound to DNA as a tetramer, the results suggest a model in which two of the p4 subunits interact with the DNA, bending it, while the other two subunits remain accessible to interact with RNA polymerase.
Purification of recombinant Chlamydia trachomatis histone H1‐like protein Hc2, and comparative functional analysis of Hc2 and Hc1
Authors: Pedersen Lotte Bang , Birkelund Svend , Christiansen Gunna 
Published: October 2006

SummaryThe metabolically inactive developmental form of Chlamydia trachomatis, the elementary body, contains two very basic DNA‐binding proteins with homology to eukaryotic histone H1. One of these, Hc1, is relatively well characterized and induces DNA condensation in vitro, whereas the other, Hc2, is functionally virtually uncharacterized. In this study we describe the purification of Hc2, and a detailed comparative functional analysis of Hc2 and Hc1 is presented. By gel shift assays and electron microscopy, marked differences in the nucleic acid‐binding properties of Hc2 and Hc1 were observed. Furthermore, Hc2 was found to strongly inhibit translation and transcription in vitro. Our results imply that DNA condensation is not the only function of Hc2.
Tandem genes encode cell‐surface polypeptides SspA and SspB which mediate adhesion of the oral bacterium Streptococcus gordonii to human and bacterial receptors
Authors: Demuth Donald R. , Duan Yang , Brooks Wanda , Holmes Ann R. , McNab Roderick , Jenkinson Howard F. 
Published: October 2006

SummaryThe highly conserved antigen I/II family of polypeptides produced by oral streptococci are believed to be colonization determinants and may mediate adhesion of bacterial cells to salivary glycoproteins adsorbed to cells and tissues in the human oral cavity. Streptococcus gordonii is shown to express, on the cell surface, two antigen I/II polypeptides designated SspA and SspB (formerly Ssp‐5) that are the products of tandemly arranged chromosomal genes. The structure and arrangement of these genes is similar in two independently isolated strains, DL1 and M5, of S. gordonii. The mature polypeptide sequences of M5 SspA (1539 amino acid (aa) residues) and SspB (1462 aa residues) are almost wholly conserved (98% identical) in the C‐terminal regions (from residues 796 in SspA and 719 in SspB, to the respective C‐termini), well‐conserved (84%) at the N‐terminal regions (residues 1–429), and divergent (only 27% identical residues) within the intervening central regions. Insertional inactivation of the sspA gene in S. gordonii DL1 resulted in reduced binding of cells to salivary agglutinin glycoprotein (SAG), human erythrocytes, and to the oral bacterium Actinomyces naeslundii. Further reductions in streptococcal cell adhesion to SAG and to two strains of A. naeslundii were observed when both sspA and sspB genes were inactivated. The results suggest that both SspA and SspB polypeptides are involved in adhesion of S. gordonii cells to human and bacterial receptors.
Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI‐anchored plasma membrane
Authors: Donzeau Mariel , Bourdineaud Jean‐Paul , Lauquin Guy J.‐M. 
Published: October 2006

SummaryExpression of the yeast Saccharomyces cerevisiae SRP1 (serine‐rich protein) gene is shown here to be induced both‐ by low temperature and anaerobic growth conditions. We show that anaerobic SRP1 expression is haem‐dependent; however, haem influence does not operate through the action of the hypoxic‐gene ROX1 repressor. The SRP1 promoter region displaying the stress‐responsive elements is restricted to its first 551 bp, upstream of the initiation codon, although an upstream activation site contained in upstream sequences is required for full promoter activity. In addition, we demonstrate that the TIP1 gene, sharing similar nucleotide and polypeptide structure with SRP1, and previously reported to be a cold‐shock‐inducible gene, is also a hypoxic gene. Srp1 protein production is similarly induced by low temperature and anaerobic growth conditions. This protein, detected in the plasma membrane fraction, is shown to be exposed on the cell surface via a glycosyl‐phosphatidylinositol membrane anchoring.
Bacterial cytochromes P‐450
Authors: Munro Andrew W. , Lindsay J. Gordon 
Published: October 2006

SummaryThe cytochromes P‐450 (P‐450s) constitute an extremely large family ('superfamily') of haemoproteins that catalyse the oxidation of a wide range of physiological and non‐physiological compounds. A remarkable feature of the P‐450s is the manipulation of the same basic structure and chemistry to achieve an enormous range of functions in organisms as diverse as bacteria and man. Indeed, the P‐450s have been described as ‘the most versatile biological catalyst known’. Much research is focussed on mammalian P‐450s, with their roles in such processes as steroid transformations and the metabolism of carcinogens and other xenobiotics. However, our knowledge of the structure and function of the P‐450s has been advanced by analysis of a limited number of its bacterial members, primarily P‐450cam from Pseudomonas putida. Four P‐450 structures have been solved to date, all of which are from bacterial sources. The aim of this review is to assess current knowledge of the many bacterial P‐450s, with emphasis on their diverse biological roles and on the advances in our knowledge of this extremely important enzyme class, which have been made feasible through their study.
Structural and functional analysis of aa3‐type and cbb3‐type cytochrome c oxidases of Paracoccus denitrificans reveals significant differences in proton‐pump design
Authors: de Gier Jan‐Willem L. , Schepper Mike , Reijnders Willem N. M. , van Dyck Stef J. , Slotboom Dirk Jan , Warne Antony , Saraste Matti , Krab Klaas , Finel Moshe , Stouthamer Adriaan H. , van Spanning Rob J. M. , van der Oost John 
Published: October 2006

SummaryIn Paracoccusdenitrificans the aa3‐type cytochrome c oxidase and the bb3‐type quinol oxidase have previously been characterized in detail, both biochemically and genetically. Here we report on the isolation of a genomic locus that harbours the gene cluster ccoNOQP, and demonstrate that it encodes an alternative cbb3‐type cytochrome c oxidase. This oxidase has previously been shown to be specifically induced at low oxygen tensions, suggesting that its expression is controlled by an oxygen‐sensing mechanism. This view is corroborated by the observation that the ccoNOQP gene cluster is preceded by a gene that encodes an FNR homologue and that its promoter region contains an FNR‐binding motif. Biochemical and physiological analyses of a set of oxidase mutants revealed that, at least under the conditions tested, cytochromes aa3, bb3. and cbb3 make up the complete set of terminal oxidases in P. denitrificans. Proton‐translocation measurements of these oxidase mutants indicate that all three oxidase types have the capacity to pump protons. Previously, however, we have reported decreased H+/e coupling efficiencies of the cbb3‐type
The 4784V missense mutation of the dnaA5 and dnaA46 alleles confers a defect in ATP binding and thermoiability in initiation of Escherichia coli DNA replication
Authors: Carr Kevin M. , Kaguni Jon M. 
Published: October 2006

Summary The temperature‐sensitive dnaA5 and dnaA46 alleles each contain two missense mutations. These mutations have been separated and the resulting mutant proteins studied with regard to their role in initiation of DNA replication in vitro. Whereas the His‐252 to tyrosine substitution (H252Y) unique to the dnaA46 allele did not affect the activities of DnaA protein, the unique substitution of the dnaAS allele, Gly‐426 to serine (G426S), was reduced in its DNA‐binding affinity for oriC, the chromosomal origin. This suggests that the C‐terminal region of the DnaA protein is involved in DNA binding. The alanine‐to‐valine substitution at amino acid 184 (A184V) that is common to both of the alleles is responsible for the thermolabile defect and lag in DNA synthesis of these mutants. Mutant proteins bearing the common substitution were defective in ATP binding and were inactive in a replication system reconstituted with purified proteins. DnaK and GrpE protein activated these mutant proteins for replication and ATP binding; the latter was measured indirectly by the ATP‐dependent formation of a tryp‐sin‐resistant peptide. However, with this assay, the ATP‐binding affinity appeared to be reduced relative to wild‐type DnaA protein. Activation was by conversion of a self‐aggregate to the monomer, and also by a conformational alteration that correlated with ATP binding.
Dual regulation of the paraquat‐inducible gene pqi‐5 by SoxS and RpoS in Escherichia coli
Authors: Koh Young‐Sang , Roe Jung‐Hye 
Published: October 2006

Summary The pqi‐5 gene, producing a probable membrane protein of unknown function, has been reported to be a member of the soxRS regulon. The SoxRS‐dependent induction of pqi‐5 by paraquat occurs only during the exponential phase. The expression of pqi‐5 increased in the absence of paraquat during the stationary phase or under conditions of carbon or phosphate starvation. This increase was regulated at the transcriptional level by RpoS (σs), which recognized the second promoter (P2) approx. 5 nucleotides upstream from the promoter (P1) used at the exponential phase. Studies with a series of 5’deletions revealed that the paraquat‐responsive element resides between ‐52 and ‐42 nucleotides upstream from the P1 start site, whose nucleotide sequence matches closely to other SoxS‐binding sequences. The stationary‐phase induction required sequences up to position ‐42, which correspond to the 5’border of the putative ‐35 hexamer for the P2 promoter. The binding of the purified SoxS protein to the pqi‐5 promoter upstream sequences was demonstrated by gel mobility‐shift and DNase I protection assays. The transcription from P1 promoter by EσD was activated by purified SoxS in vitro, as was observed in vivo. The dual regulation of pqi‐5 by SoxS at the exponential phase and RpoS at the stationary phase is the first to be reported among the members of the soxRS regulon, suggesting that this gene might indeed play some role under stressful conditions.
Effect of O side‐chain length and composition on the virulence of Shigella flexneri 2a
Authors: Sandlin Robin C. , Goldberg Marcia B. , Maurelli Anthony T. 
Published: October 2006

SummaryIcsA of Shigella flexneri is required for intercellular spread and is located in the outer membrane at one pole of the bacterium, where it catalyses the polymerization of host‐cell actin. The formation of the actin tail provides the force to move the bacterium in a unidirectional manner through the host‐cell cytoplasm. We have previously demonstrated that rough lipopolysaccharide (LPS) mutants of S. flexneri 2a are avirulent and cannot form plaques in tissue‐culture monolayers. This inability to form plaques is associated with non‐polar localization of IcsA and loss of host‐cell membrane‐protrusion formation ('fireworks'). To define the minimal LPS structure required for fireworks formation, we constructed a strain of S. flexneri (BS497) that contains a mutation in rfc, encoding the O side‐chain polymerase, and a strain, BS520, that possesses a defective O side‐chain ligase due to a mutation in rfaL. BS497 produces a LPS that consists of a core with one repeat unit of the O side‐chain, while BS520 produces a LPS consisting of a complete core with no O side‐chain. BS497 remained invasive but did not form fireworks or plaques in tissue‐culture monolayers and was negative in the Serény test. BS520 was invasive, generated reduced numbers of short fireworks, and made tiny plaques, but it was negative in the Serény test. Analysis of BS497 with anti‐lcsA antibody demonstrated that IcsA was distributed over the entire cell surface. The distribution of IcsA on the surface of BS520 was predominantly unipolar, with some trail‐back of IcsA label along the sides of the bacterium. A similar pattern was seen when infected monolayers were stained for polymerized actin. These results suggest that both the presence and the length of the O side‐chain are important in the proper localization or maintenance of IcsA at the pole which subsequently affects the ability to form actin tails and produce fireworks. This reduced ability to form actin tails and fireworks results in a decreased ability of Shigella to move into adjacent host cells. To determine if the sugar composition of the O side‐chain is important in the ability to form fireworks, the rfb region of S. flexneri2a was replaced with the rfb region from Escherichia coll serotype O8 or O25. Both hybrids were invasive, formed plaques, and gave positive Serény reactions. These results suggest that, unlike LPS length, the sugar composition of the O side‐chain is not a critical requirement for the proper localization of IcsA and efficient intercellular movement.
Vacuolar H+‐ATPase and weak base action in Dictyostelium
Authors: Davies L. , Farrar N. A. , Satre M. , Dottin R. P. , Gross J. D. 
Published: October 2006

Summary Amoebae of Dictyostelium discoideum release ammonia during development, and the accumulation of this weak base is believed to be responsible for inhibiting fruiting‐body formation and switching aggregates into migrating slugs. Exposure to weak bases can also inhibit aggregation and cell‐type specific gene expression. The pathway by which weak bases influence development is not understood. We show here that the development of a set of mutants defective in acidification of intracellular acidic compartments is abnormally sensitive to inhibition by weak bases. Moreover even in the absence of added weak bases these mutants are delayed in aggregation and have a protracted migratory phase. The same behaviour is observed in trans‐formants harbouring an antisense construct for one of the vacuolar H+‐ATPase subunits. These results support the idea that weak bases exert their effects by inhibiting acidification of an intracellular acidic compartment.
Interleukin‐21 Induces T‐cell Activation and Proinflammatory Cytokine Secretion in Rheumatoid Arthritis
Authors: Li J. , Shen W. , Kong K. , Liu Z. 
Published: October 2006

AbstractInterleukin (IL)‐21 is a CD4+ T‐cell‐derived cytokine, which is involved in innate and adaptive immune response. In this study, we analysed IL‐21 receptor (IL‐21R) expression in peripheral blood and synovial fluid mononuclear cells, and investigated the role of IL‐21 in the induction of proinflammatory cytokine production by peripheral blood T cells (PB‐T) and synovial fluid T cells (SF‐T) from patients with rheumatoid arthritis (RA). Immunohistochemical staining demonstrated that IL‐21R‐positive cells were significantly increased in inflamed synovial tissues of RA patients compared with osteoarthritis (OA) and healthy controls. Flow cytometric analysis confirmed that IL‐21R was mainly expressed in freshly isolated CD4, CD8, B and NK cells from peripheral blood and synovial fluid, but decreased gradually in T cells 24 h after anti‐CD3 stimulation. PB‐ and SF‐T cells from RA patients were more responsive to IL‐21 when compared with controls. Importantly, isolated PB‐ or SF‐T cells from RA patients, when stimulated with IL‐21 and anti‐CD3 MoAb, secreted markedly higher levels of TNF‐α and IFN‐γ than controls. These data indicate that IL‐21R is overexpressed in the inflamed synovial membrane and in peripheral blood or synovial fluid leukocytes of RA patients, and that IL‐21 enhances local T‐cell activation, proliferation and proinflammatory cytokine secretion. Thus, blockade of IL‐21R signalling pathway may have a therapeutic potential in acute RA patients.
FURTHERING INJUSTICES AGAINST WOMEN: GENETIC INFORMATION, MORAL OBLIGATIONS, AND GENDER
Authors: DE MELO‐MARTÍN INMACULADA 
Published: October 2006

ABSTRACTThe purpose of this paper is to show that a decontextualized approach to ethical issues is not just unhelpful for the decision making process of real, situated human beings, but dangerous. This is so, because by neglecting the context in which people make moral decisions we run the risk of reinforcing or furthering injustices against already disadvantaged groups. To show this, I evaluate three moral obligations that our ability to obtain genetic information has made salient: the duty to obtain genetic information about ourselves, the obligation to inform family members about genetic risks and the duty not to reproduce when we know that there is a high risk of transmitting a serious disease or defect. I will argue here that in ignoring the context in which these moral obligations are put into practice, and in particular the situation of women in our society, those who defend these moral duties might be furthering injustices against women.