bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometry of the species–area relationship in central European birds: testing the mechanism
Authors: Storch David , Izling Arnošt L. , Gaston Kevin J. 
Published: May 2003

SummaryThe species–area relationship (SAR) is one of the major patterns in community ecology, but the mechanisms that contribute to its exact shape have remained obscure. In continuous mainland areas, the SAR has been attributed to sampling effects (large areas contain species that are too rare to be present in small areas), habitat heterogeneity (large areas contain more types of habitat allowing more species to coexist), and population and metapopulation processes causing spatial aggregation. We tested the contribution of these effects to SARs using data on breeding bird distributions in the Czech Republic, their total population sizes and spatial distributions of their preferred habitats.2. The relationship between number of species and sampled area is more or less linear on a log–log scale within the Czech Republic, although it reveals saturation when the area is expanded to the whole of central Europe.Neither sampling effect nor habitat heterogeneity alone explain the observed SAR shape: both models predict much higher species richness within any area and a SAR of much lower slope than observed.A combined model based on random sampling constrained by the amount of suitable habitat within an area gives quite realistic predictions of species numbers within different sample areas. Nevertheless, the observed pattern reveals much higher variance of species richness amongst areas, species often being significantly more spatially aggregated than predicted by habitat distribution.Moreover, the relationship between the amount of suitable habitat and the probability of quadrat occupancy is actually nonsignificant for about two‐thirds of species, indicating that assumptions of the combined model are unrealistic. Therefore, the shape and slope of SARs are actually affected both by habitat heterogeneity that represents the major driver of distribution of some species, and by spatial aggregation that is not attributable to habitat heterogeneity in other species.
Small non‐coding RNAs, co‐ordinators of adaptation processes in Escherichia coli: the RpoS paradigm
Authors: Repoila F. , Majdalani N. , Gottesman S. 
Published: May 2003

SummaryAdaptation to the changing environment requires both the integration of external signals and the co‐ordination of internal responses. Around 50 non‐coding small RNAs (sRNAs) have been described in Escherichia coli; the levels of many of these vary with changing environmental conditions. This suggests that they play a role in cell adaptation. In this review, we use the regulation of RpoS (σ38) translation as a paradigm of sRNA‐mediated response to environmental conditions; rpoS is currently the only known gene regulated post‐transcriptionally by at least three sRNAs. DsrA and RprA stimulate RpoS translation in response to low temperature and cell surface stress, respectively, whereas OxyS represses RpoS translation in response to oxidative shock. However, in addition to regulating RpoS translation, DsrA represses the translation of HNS (a global regulator of gene expression), whereas OxyS represses the translation of FhlA (a transcriptional activator), allowing the cell to co‐ordinate different pathways involved in cell adaptation. Environmental cues affect the synthesis and stability of specific sRNAs, resulting in specific sRNA‐dependent translational control.
Evidence that acetyl phosphate functions as a global signal during biofilm development
Authors: Wolfe Alan J. , Chang Dong‐Eun , Walker Jason D. , Seitz‐Partridge Jeanine E. , Vidaurri Michael D. , Lange Charles F. , Prüß Birgit M. , Henk Margaret C. , Larkin John C. , Conway Tyrrell 
Published: May 2003

SummaryWe used DNA macroarray analysis to identify genes that respond to the status of the intracellular acetyl phosphate (acP) pool. Genes whose expression correlated negatively with the ability to synthesize acP (i.e. negatively regulated genes) function primarily in flagella biosynthesis, a result consistent with observations that we published previously (Prüß and Wolfe, 1994, Mol Microbiol 12: 973–984). In contrast, genes whose expression correlated positively with the ability to synthesize acP (i.e. positively regulated genes) include those for type 1 pilus assembly, colanic acid (capsule) biosynthesis and certain stress effectors. To our knowledge, this constitutes the first report that these genes may respond to the status of the intracellular acP pool. Previously, other researchers have implicated flagella, type 1 pili, capsule and diverse stress effectors in the formation of biofilms. We therefore tested whether cells altered in their ability to metabolize acP could construct normal biofilms, and found that they could not. Cells defective for the production of acP and cells defective for the degradation of acP could both form biofilms, but these biofilms exhibited characteristics substantially different from each other and from biofilms formed by their wild‐type parent. We confirmed the role of individual cell surface structures, the expression of which appears to correlate with acP levels, in fim or fli mutants that cannot assemble type 1 pili or flagella respectively. Thus, the information gained by expression profiling of cells with altered acP metabolism indicates that acP may help to co‐ordinate the expression of surface structures and cellular processes involved in the initial stages of wild‐type biofilm development.
PY54, a linear plasmid prophage of Yersinia enterocolitica with covalently closed ends
Authors: Hertwig Stefan , Klein Iris , Lurz Rudi , Lanka Erich , Appel Bernd 
Published: May 2003

SummaryPY54 is a temperate phage isolated from Yersinia enterocolitica. Lysogenic Yersinia strains harbour the PY54 prophage as a plasmid (pY54). The plasmid has the same size (46 kb) as the PY54 genome isolated from phage particles. By electron microscopy, restriction analysis and DNA sequencing, it was demonstrated that the phage and the plasmid DNAs are linear, circularly permuted molecules. Unusually for phages of Gram‐negative bacteria, the phage genome has 3′‐protruding ends. The linear plasmid pY54 has covalently closed ends forming telomere‐like hairpins. The equivalent DNA sequence of the phage genome is a 42 bp perfect palindrome. Downstream from the palindrome, an open reading frame (ORF) was identified that revealed strong DNA homology to the telN gene of Escherichia coli phage N15 encoding a protelomerase. Similar to PY54, the N15 prophage is a linear plasmid with telomeres. The N15 protelomerase has cleaving/joining activity generating the telomeres by processing a 56 bp palindrome (telomere resolution site tel RL). To study the activity of the PY54 protein, the telN‐like gene was cloned and expressed in E. coli. A 77 kDa protein was obtained and partially purified. The protein was found to process recombinant plasmids containing the 42 bp palindrome. Telomere resolution of plasmids under in vivo conditions was also investigated in Yersinia infected with PY54. Processing required a plasmid containing the palindrome as well as adjacent DNA sequences from the phage including an additional inverted repeat. Regions on the phage genome important for plasmid maintenance were defined by the construction of linear and circular miniplasmid derivatives of pY54, of which the smallest miniplasmid comprises a 4.5 kb DNA fragment of the plasmid prophage.
Region 4 of σ as a target for transcription regulation
Authors: Dove Simon L. , Darst Seth A. , Hochschild Ann 
Published: May 2003

SummaryBacterial σ factors play a key role in promoter recognition, making direct contact with conserved promoter elements. Most σ factors belong to the σ70 family, named for the primary σ factor in Escherichia coli. Members of the σ70 family typically share four conserved regions and, here, we focus on region 4, which is directly involved in promoter recognition and serves as a target for a variety of regulators of transcription initiation. We review recent advances in the understanding of the mechanism of action of regulators that target region 4 of σ.
Identification and macrophage‐activating activity of glycolipids released from intracellular Mycobacterium bovis BCG
Authors: Rhoades E. , Hsu F‐. F. , Torrelles J. B. , Turk J. , Chatterjee D. , Russell D. G. 
Published: May 2003

SummaryIntracellular mycobacteria release cell wall glycolipids into the endosomal network of infected macrophages. Here, we characterize the glycolipids of Mycobacterium bovis BCG (BCG) that are released into murine bone marrow‐derived macrophages (BMMØ). Intracellularly released mycobacterial lipids were harvested from BMMØ that had been infected with 14C‐labelled BCG. Released BCG lipids were resolved by thin‐layer chromatography, and they migrated similarly to phosphatidylinositol dimannosides (PIM2), mono‐ and diphosphatidylglycerol, phosphatidylethanolamine, trehalose mono‐ and dimycolates and the phenolic glycolipid, mycoside B. Culture‐derived BCG lipids that co‐migrated with the intracellularly released lipids were purified and identified by electrospray ionization mass spectrometry. When delivered on polystyrene microspheres, fluorescently tagged BCG lipids were also released into the BMMØ, in a manner similar to release from viable or heat‐killed BCG bacilli. To determine whether the released lipids elicited macrophage responses, BCG lipid‐coated microspheres were delivered to interferon gamma‐primed macrophages (BMMØ or thioglycollate‐elicited peritoneal macrophages), and reactive nitrogen intermediates as well as tumour necrosis factor‐alpha and monocyte chemoattractant protein‐1 production were induced. When fractionated BCG lipids were delivered on the microspheres, PIM2 species reproduced the macrophage‐activating activity of total BCG lipids. These results demonstrate that intracellular mycobacteria release a heterogeneous mix of lipids, some of which elicit the production of proinflammatory cytokines from macrophages that could potentially contribute to the granulomatous response in tuberculous diseases.
Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli
Authors: Inoue Koichi , Alsina Janivette , Chen Jingqiu , Inouye Masayori 
Published: May 2003

SummaryEra is a small GTP‐binding protein and essential for cell growth in Escherichia coli. It consists of two domains: N‐terminal GTP‐binding and C‐terminal RNA‐binding KH domains. It has been shown to bind to 16S rRNAs and 30S ribosomal subunits in vitro. Here, we report that a precursor of 16S rRNA accumulates in Era‐depleted cells. The accumulation of the precursors is also seen in a cold‐sensitive mutant, E200K, in which the mutation site is located in the C‐terminal domain. The major precursor molecule accumulated seems to be 17S rRNA, containing extra sequences at both 5′ and 3′ ends of 16S rRNA. Moreover, the amounts of both 30S and 50S ribosomal subunits relative to the amount of 70S monosomes increase in Era‐depleted and E200K mutant cells. The C‐terminal KH domain has a high structural similarity to the RbfA protein, a cold shock protein that also specifically associates with 30S ribosomal subunits. RbfA is essential for cell growth at low temperature, and a precursor of 16S rRNA accumulates in an rbfA deletion strain. The 16S rRNA precursor seems to be identical in size to that accumulated in Era mutant cells. Surprisingly, the cold‐sensitive cell growth of the rbfA deletion cells was partially suppressed by overproduction of the wild‐type Era. The C‐terminal domain alone was not able to suppress the cold‐sensitive phenotype, whereas Era‐dE, which has a 10‐residue deletion in a putative effector region of the N‐terminal domain, functioned as a more efficient suppressor than the wild‐type Era. It was found that Era‐dE suppressed defective 16S rRNA maturation, resuming a normal polysome profile to reduce highly accumulated free 30S and 50S subunits in the rbfA deletion cells. These results indicate that Era is involved in 16S rRNA maturation and ribosome assembly.
Antagonism of PII signalling by the AmtB protein of Escherichia coli
Authors: Blauwkamp Timothy A. , Ninfa Alexander J. 
Published: May 2003

Summary Escherichia coli AmtB is a member of the MEP/Amt family of ammonia transporters found in archaea, eubacteria, fungi, plants and animals. In prokaryotes, AmtB homologues are co‐transcribed with a PII paralogue, GlnK, in response to nitrogen limitation. Here, we show that AmtB antagonizes PII signalling through NRII and that co‐expression of GlnK with AmtB overcomes this antagonism. In cells lacking GlnK, expression of AmtB during nitrogen starvation prevented deinduction of Ntr gene expression when a nitrogen source became available. The absence of AmtB in cells lacking GlnK allowed rapid reduction of Ntr gene expression during this transition, indicating that one function of GlnK is to prevent AmtB‐mediated antagonism of PII signalling after nitrogen starvation. Other roles of GlnK in controlling Ntr gene expression and maintaining viability during nitrogen starvation were unaffected by AmtB. Expression of AmtB from a constitutive promoter under nitrogen‐rich conditions induced full expression of glnALG and elevated expression of glnK in wild‐type and glnK cells; thus, the ability of AmtB to raise Ntr gene expression did not require a factor found only in nitrogen‐starved cells. Experiments with intact cells showed that AmtB acted downstream of a uridylyl transferase uridylyl‐removing enzyme (UTase/UR) and upstream of NRII, suggesting that the target was PII. AmtB also slowed the deuridylylation of PII∼UMP upon ammonia addition, showing that multiple PII interactions were affected by AmtB. Our data are consistent with a hypothesis that AmtB interacts with PII and GlnK, and that co‐transcription of glnK and amtB prevents titration of PII when AmtB is highly expressed.
Medicinal genetics approach towards identifying the molecular target of a novel inhibitor of fungal cell wall assembly
Authors: Tsukahara Kappei , Hata Katsura , Nakamoto Kazutaka , Sagane Koji , Watanabe Nao‐aki , Kuromitsu Junro , Kai Junko , Tsuchiya Mamiko , Ohba Fuminori , Jigami Yoshifumi , Yoshimatsu Kentaro , Nagasu Takeshi 
Published: May 2003

SummaryGlycosylphosphatidylinositol (GPI)‐anchored cell wall mannoproteins are required for the adhesion of pathogenic fungi, such as Candida albicans, to human epithelium. Small molecular inhibitors of the cell surface presentation of GPI‐anchored mannoproteins would be promising candidate drugs to block the establishment of fungal infections. Here, we describe a medicinal genetics approach to identifying the gene encoding a novel target protein that is required for the localization of GPI‐anchored cell wall mannoproteins. By means of a yeast cell‐based screening procedure, we discovered a compound, 1‐[4‐butylbenzyl]isoquinoline (BIQ), that inhibits cell wall localization of GPI‐anchored mannoproteins in Saccharomyces cerevisiae. Treatment of C. albicans cells with this compound resulted in reduced adherence to a rat intestine epithelial cell monolayer. A previously uncharacterized gene YJL091c, named GWT1, was cloned as a dosage‐dependent suppressor of the BIQ‐induced phenotypes. GWT1 knock‐out cells showed similar phenotypes to BIQ‐treated wild‐type cells in terms of cell wall structure and transcriptional profiles. Two different mutants resistant to BIQ each contained a single missense mutation in the coding region of the GWT1 gene. These results all suggest that the GWT1 gene product is the primary target of the compound.
Identification of a 5‐nucleotide sequence that controls expression of the ica locus in Staphylococcus aureus and characterization of the DNA‐binding properties of IcaR
Authors: Jefferson Kimberly K. , Cramton Sarah E. , Götz Friedrich , Pier Gerald B. 
Published: May 2003

SummaryBiofilm formation is an important aspect of the pathogenesis of staphylococcal infections. A β‐1,6‐linked N‐acetyl glucosamine polysaccharide is critical to biofilm elaboration and is synthesized by proteins encoded by the intercellular adhesion (ica) locus. These studies were undertaken to characterize the mechanism by which transcription of the ica locus in S. aureus is regulated using isogenic S. aureus MN8 and MN8 mucoid (MN8m) strains, the latter of which constitutively overproduces biofilm. Transformation of the ica locus from MN8m to the ica knock‐out mutants of two strains, MN8 and NCTC 10833, conferred a strong biofilm‐producing phenotype. Sequence analysis revealed a 5‐nucleotide deletion within the promoter region of the ica locus in MN8m compared with the sequence in the wild‐type locus. Deletion or substitution of these 5 nucleotides within the wild‐type ica locus augmented transcription of the ica locus and induced the strong biofilm‐producing phenotype. Gel shift analysis demonstrated that a protein(s) within cell‐free lysates from strain MN8 bind(s) specifically to oligonucleotides representative of the wild‐type ica promoter sequence and that this binding is greatly diminished by the deletion or substitution of the 5 nucleotides. DNase I footprint analysis revealed that purified IcaR, thought to be a regulator of ica transcription, also binds to the ica promoter sequence just upstream of the ica start codon, but its affinity for the ica promoter is unaffected by deletion of the 5‐nucleotide motif. These findings identify a 5‐nucleotide motif within the ica promoter region that has a functional role in transcriptional regulation of the ica locus that is independent of IcaR, and also show that IcaR binds to the promoter region of the S. aureus ica locus.
Sequence‐specific recognition but position‐dependent cleavage of two distinct telomeres by the Borrelia burgdorferi telomere resolvase, ResT
Authors: Tourand Yvonne , Kobryn Kerri , Chaconas George 
Published: May 2003

SummaryAn unusual feature of bacteria in the genus Borrelia (causative agents of Lyme disease and relapsing fever) is a segmented genome consisting of multiple linear DNA molecules with covalently closed hairpin ends, known as telomeres. The hairpin telomeres are generated by a DNA breakage and reunion process (telomere resolution) promoted by ResT, an enzyme using an active site related to that of tyrosine recombinases and type IB topoisomerases. In this study, we define the minimal sequence requirements for a functional telomere and identify specific basepairs that appear to be important for telomere resolution. In addition, we show that the two naturally occurring and distinct telomere spacings found in B. burgdorferi can both be efficiently processed by ResT. This flexibility for substrate utilization by ResT supports the argument for a single telomere resolvase in Borrelia. Furthermore, although telomere recognition requires sequence specificity in part of the substrate, DNA cleavage is instead position dependent and occurs at a fixed distance from the axis of symmetry and the conserved sequence of box 3 in the different replicated telomere substrates. This positional dependence for DNA cleavage has not been observed previously for a tyrosine recombinase.
Substrate specificity of type III flagellar protein export in Salmonella is controlled by subdomain interactions in FlhB
Authors: Fraser Gillian M. , Hirano Takanori , Ferris Hedda U. , Devgan Lara L. , Kihara May , Macnab Robert M. 
Published: May 2003

SummaryFlhB, an integral membrane protein, gates the type III flagellar export pathway of Salmonella. It permits export of rod/hook‐type proteins before hook completion, whereupon it switches specificity to recognize filament‐type proteins. The cytoplasmic C‐terminal domain of FlhB (FlhBC) is cleaved between Asn‐269 and Pro‐270, defining two subdomains: FlhBCN and FlhBCC. Here, we show that subdomain interactions and cleavage within FlhB are central to substrate‐specificity switching. We found that deletions between residues 216 and 240 of FlhBCN permitted FlhB cleavage but abolished function, whereas a deletion spanning Asn‐269 and Pro‐270 abolished both. The mutation N269A prevented cleavage at the FlhBCN–FlhBCC boundary. Cells producing FlhB(N269A) exported the same amounts of hook‐capping protein as cells producing wild‐type FlhB. However, they exported no flagellin, even when the fliC gene was being expressed from a foreign promoter to circumvent regulation of expression by FlgM, which is itself a filament‐type substrate. Electron microscopy revealed that these cells assembled polyhook structures lacking filaments. Thus, FlhB(N269A) is locked in a conformation specific for rod/hook‐type substrates. With FlhB(P270A), cleavage was reduced but not abolished, and cells producing this protein were weakly motile, exported reduced amounts of flagellin and assembled polyhook filaments.
A LuxR‐type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes
Authors: Pappas Katherine M. , Winans Stephen C. 
Published: May 2003

SummaryTraR, a LuxR‐type quorum‐sensing transcription factor in Agrobacterium tumefaciens, activates genes required for conjugal transfer of the Ti plasmid and also enhances the copy number of a nopaline‐type Ti plasmid. Here, we show that TraR increases the copy number of an octopine‐type Ti plasmid up to eightfold and that TraR activates transcription of the repABC operon up to 25‐fold. The ability of TraR to increase copy number was strictly dependent on several TraR‐activated promoters of this operon, indicating that TraR affects copy number solely at the level of transcription. Promoter resections and mRNA transcript analysis revealed the presence of three TraR‐dependent promoters. Two TraR‐dependent transcription start sites are located 45.5 and 65.5 nucleotides downstream of a site called tra box II, whereas the third start site lies 42.5 nucleotides downstream of a site called tra box III. Purified TraR bound to both tra boxes with comparable affinities, causing moderate DNA bending. TraR bound and bent these two sites independently rather than synergistically. Alteration of tra box III to match the consensus sequence dramatically increased TraR‐dependent expression of repABC and plasmid copy number. TraR‐dependent elevation of Ti plasmid copy number caused a three‐ to fourfold increase in plant tumorigenesis.