bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial phylogeography of the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region
Authors: Michaux J. R. , Magnanou E. , Paradis E. , Nieberding C. , Libois R. 
Published: March 2003

AbstractWe sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) collected from 40 European localities. The aims of the study were to answer the following questions. (i) Did the Mediterranean peninsulas play a role as refuge for woodmice? (ii) Is genetic variability of A. sylvaticus higher in the Mediterranean region compared with northern Europe? (iii) Are the patterns of the postglacial colonization of Europe by woodmice similar to those presently recognized for other European species? The results provide a clear picture of the impact of the Quaternary glaciations on the genetic and geographical structure of the woodmouse. Our analyses indicate a higher genetic variability of woodmice in the Mediterranean peninsulas compared to northern Europe, suggesting a role of the former as refuge regions for this small mammal. An original pattern of postglacial colonization is proposed where the Iberian and southern France refuge populations colonized almost all European regions. The Sicilian population appears to be very differentiated and highly variable. This emphasizes the importance of this island as a ‘hot spot’ for the intraspecific genetic diversity of the woodmouse. Finally, woodmice in North Africa originated from southwestern Europe, most probably as a result of a recent anthropogenic introduction.
Genetic divergence between cave and surface populations of Astyanax in Mexico (Characidae, Teleostei)
Authors: Strecker U. , Bernatchez L. , Wilkens H. 
Published: March 2003

AbstractA study of genetic diversity at microsatellite loci and the mitochondrial DNA (mtDNA) cytochrome b gene was carried out to assess genetic relationships among four Mexican cave (Pachon, Sabinos, Tinaja, Chica) and four surface populations of Astyanax fasciatus (Characidae) from northeast Mexico and the Yucatan. With the exception of Chica, the cave populations were all characterized by extremely low microsatellite variability, which most likely resulted from bottleneck events. Population analyses of the microsatellite data indicated no measurable levels of gene flow between all cave and surface populations (FST > 0.0707). Phylogenetic analyses of mtDNA data showed that only two cave populations — Sabinos and Tinaja — group together to the exclusion of surface populations. From the microsatellite data these cave populations cluster with the Pachon cave fish population. The mtDNA thus appears to have been replaced in Pachon because of introgressive hybridization. It is likely that these three cave populations have descended from a surface ancestor in common with current surface populations, rather than evolving recently from one of the extant surface populations. Like Pachon, the Chica population clustered with the surface populations according to mtDNA data, but was not clearly associated with either the surface or the other cave populations according to the microsatellite data. Our data indicate that the Chica population evolved recently from a surface population, and subsequently hybridized with a phylogenetically older cave population. In conclusion, both the microsatellite and mtDNA data suggest multiple origins of cave populations and the Chica and Sabinos/Tinaja/Pachon were founded after at least two independent invasions from surface populations.
Pollen dispersal of tropical trees (Dinizia excelsa: Fabaceae) by native insects and African honeybees in pristine and fragmented Amazonian rainforest
Authors: Dick Christopher W. , Etchelecu Gabriela , Austerlitz Frédéric 
Published: March 2003

AbstractTropical rainforest trees typically occur in low population densities and rely on animals for cross‐pollination. It is of conservation interest therefore to understand how rainforest fragmentation may alter the pollination and breeding structure of remnant trees. Previous studies of the Amazonian tree Dinizia excelsa (Fabaceae) found African honeybees (Apis mellifera scutellata) as the predominant pollinators of trees in highly disturbed habitats, transporting pollen up to 3.2 km between pasture trees. Here, using microsatellite genotypes of seed arrays, we compare outcrossing rates and pollen dispersal distances of (i) remnant D. excelsa in three large ranches, and (ii) a population in undisturbed forest in which African honeybees were absent. Self‐fertilization was more frequent in the disturbed habitats (14%, n = 277 seeds from 12 mothers) than in undisturbed forest (10%, n = 295 seeds from 13 mothers). Pollen dispersal was extensive in all three ranches compared to undisturbed forest, however. Using a twogener analysis, we estimated a mean pollen dispersal distance of 1509 m in Colosso ranch, assuming an exponential dispersal function, and 212 m in undisturbed forest. The low effective density of D. excelsa in undisturbed forest (∼0.1 trees/ha) indicates that large areas of rainforest must be preserved to maintain minimum viable populations. Our results also suggest, however, that in highly disturbed habitats Apis mellifera may expand genetic neighbourhood areas, thereby linking fragmented and continuous forest populations.
Inbreeding depression influences genet size distribution in a marine angiosperm
Authors: Hämmerli A. , Reusch T. B. H. 
Published: March 2003

AbstractAlthough inbreeding depression is a major genetic phenomena influencing individual fitness, it is difficult to measure in wild populations. An alternative approach is to correlate heterozygosity, measured using highly polymorphic markers, with a fitness‐correlated trait. In clonal plants, genet size is predicted to be fitness correlated. Here we test the prediction that the genet size distribution of the marine clonal plant Zostera marina (eelgrass) is influenced by inbreeding depression. We used nine polymorphic microsatellite markers to access the fine scale clonal structure and to measure individual heterozygosity within 4 plots (each corresponds to 256 m2, sampled at 1‐m intervals) in two populations along the German Baltic Coast. The same plots were also sampled for flowering and vegetative shoots to obtain estimates for sexual reproductive output at the level of the genetic individual. We found substantial differences in the genet size distribution between the two populations that may be explained by different disturbance frequency. In both populations, clone size was significantly positively correlated with the total number of flowering shoots, indicating that larger clones have a higher reproductive output. Individual heterozygosity was significantly positively associated with clone size. The effect was much stronger in Falkenstein (low disturbance) than in Maasholm (high disturbance). The results indicate that in a low disturbance population the relatively outbred clones occupy a higher proportion of the available space, possibly because they outcompete relatively inbred neighbours.
Analysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C‐terminal domain of the RNA polymerase α subunit: use of alanine scanning and suppression genetics
Authors: Lee David J. , Wing Helen J. , Savery Nigel J. , Busby Stephen J. W. 
Published: March 2003

Activating Region 1 of Escherichia coli FNR protein is proposed to interact directly with the C‐terminal domain of the RNA polymerase α subunit (αCTD) during transcription activation at FNR‐regulated promoters. Using an αCTD alanine scan mutant library, we have identified the residues of αCTD that are important for FNR‐dependent transcription activation. Residues Asp‐305, Gly‐315, Arg‐317, Leu‐318 and Asp‐319 are proposed to be the key residues in the contact site on αCTD for Activating Region 1 of FNR. In previous work, it had been shown that Activating Region 1 of FNR is a large surface‐exposed patch and that the two crucial amino acid residues are Thr‐118 and Ser‐187. In this work, we have constructed Arg‐118 FNR and Arg‐187 FNR and shown that both FNR derivatives are defective in transcription activation. However, the activity of FNR carrying Arg‐118 can be partially restored by substitutions of Lys‐304 in αCTD. Similarly, the activity of FNR carrying Arg‐187 can be partially restored by substitutions of Arg‐317 or Leu‐318 in αCTD. The specificity of the restoration suggests that, during transcription activation by FNR, the side‐chain of residue 118 in Activating Region 1 of FNR is located close to Lys‐304 and Asp‐305 in αCTD. Similarly, the side‐chain of residue 187 in Activating Region 1 of FNR is located close to Arg‐317 and Leu‐318 in αCTD. These results can be used to model the interface between Activating Region 1 of FNR and its contact target in αCTD, and permit comparison of this interface with the interface between Activating Region 1 of the related transcription activator, CRP and αCTD.
Emerging strategies in microbial haem capture
Authors: Genco Caroline Attardo , Dixon Dabney White 
Published: March 2003

Gram‐negative pathogenic bacteria have evolved novel strategies to obtain iron from host haem‐sequestering proteins. These include the production of specific outer membrane receptors that bind directly to host haem‐sequestering proteins, secreted haem‐binding proteins (haemophores) that bind haem/haemoglobin/haemopexin and deliver the complex to a bacterial cell surface receptor and bacterial proteases that degrade haem‐sequestering proteins. Once removed from haem‐sequestering proteins, haem may be transported via the bacterial outer membrane receptor into the cell. Recent studies have begun to define the steps by which haem is removed from bacterial haem proteins and transported into the cell. This review describes recent work on the discovery and characterization of these systems. Reference is also made to the transport of haem in serum (via haemoglobin, haemoglobin/haptoglobin, haemopexin, albumin and lipoproteins) and to mechanisms of iron removal from the haem itself (probably via a haem oxygenase pathway in which the protoporphyrin ring is degraded). Haem protein–receptor interactions are discussed in terms of the criteria that govern protein–protein interactions in general, and connections between haem transport and the emerging field of metal transport via metallochaperones are outlined.
The X philes: structure‐specific endonucleases that resolve Holliday junctions
Authors: Sharples Gary J. 
Published: March 2003

Genetic recombination is a critical cellular process that promotes evolutionary diversity, facilitates DNA repair and underpins genome duplication. It entails the reciprocal exchange of single strands between homologous DNA duplexes to form a four‐way branched intermediate commonly referred to as the Holliday junction. DNA molecules interlinked in this way have to be separated in order to allow normal chromosome transmission at cell division. This resolution reaction is mediated by structure‐specific endonucleases that catalyse dual‐strand incision across the point of strand cross‐over. Holliday junctions can also arise at stalled replication forks by reversing the direction of fork progression and annealing of nascent strands. Resolution of junctions in this instance generates a DNA break and thus serves to initiate rather than terminate recombination. Junction resolvases are generally small, homodimeric endonucleases with a high specificity for branched DNA. They use a metal‐binding pocket to co‐ordinate an activated water molecule for phosphodiester bond hydrolysis. In addition, most junction endonucleases modulate the structure of the junction upon binding, and some display a preference for cleavage at specific nucleotide target sequences. Holliday junction resolvases with distinct properties have been characterized from bacteriophages (T4 endo VII, T7 endo I, RusA and Rap), Bacteria (RuvC), Archaea (Hjc and Hje), yeast (CCE1) and poxviruses (A22R). Recent studies have brought about a reappraisal of the origins of junction‐specific endonucleases with the discovery that RuvC, CCE1 and A22R share a common catalytic core.
Identification of the teichoic acid phosphorylcholine esterase in Streptococcus pneumoniae
Authors: Vollmer Waldemar , Tomasz Alexander 
Published: March 2003

Streptococcus pneumoniae is a major human pathogen and many interactions of this bacterium with its host appear to be mediated, directly or indirectly, by components of the bacterial cell wall, specifically by the phosphorylcholine residues which serve as anchors for surface‐located choline‐binding proteins and are also recognized by components of the host response, such as the human C‐reactive protein, a class of myeloma proteins and PAF receptors. In the present study, we describe the identification of the pneumococcal pce gene encoding for a teichoic acid phosphorylcholine esterase (Pce), an enzymatic activity capable of removing phosphorylcholine residues from the cell wall teichoic acid and lipoteichoic acid. Pce carries an N‐terminal signal sequence, contains a C‐terminal choline‐binding domain with 10 homologous repeating units similar to those found in other pneumococcal surface proteins, and the catalytic (phosphorylcholine esterase) activity is localized on the N‐terminal part of the protein. The mature protein was overexpressed in Escherichia coli and purified in a one‐step procedure by choline‐affinity chromatography and the enzymatic activity was followed using the chromophoric p‐nitrophenyl‐phosphorylcholine as a model substrate. The product of the enzymatic digestion of 3H‐choline‐labelled cell walls was shown to be phosphorylcholine. Inactivation of the pce gene in S. pneumoniae strains by insertion‐duplication mutagenesis caused a unique change in colony morphology and a striking increase in virulence in the intraperitoneal mouse model. Pce may be a regulatory element involved with the interaction of S. pneumoniae with its human host.
Cold‐regulated genes under control of the cold sensor Hik33 in Synechocystis
Authors: Suzuki Iwane , Kanesaki Yu , Mikami Koji , Kanehisa Minoru , Murata Norio 
Published: March 2003

A histidine kinase, Hik33, appears to sense decreases in temperature and to regulate the expression of certain cold‐inducible genes in the cyanobacterium Synechocystis sp. PCC6803. To examine the role of Hik33 in the regulation of gene expression, we analysed a ΔHik33 mutant using the DNA microarray technique. In wild‐type cells, genes that were strongly induced at low temperature encoded proteins that were predominantly subunits of the transcriptional and translational machinery. Most cold‐repressible genes encoded components of the photosynthetic machinery. Mutation of the hik33 gene suppressed the expression of some of these cold‐regulated genes, which could be divided into three groups according to the effect of the mutation of hik33. In the first group, regulation of gene expression by low temperature was totally abolished; in the second group, the extent of such regulation was reduced by half; and, in the third group, such regulation was totally unaffected. These results suggest that expression of the genes in the first group is regulated solely by Hik33, expression of genes in the third group is regulated by an as yet unidentified cold sensor, and expression of genes in the second group is regulated by both these cold sensors.
Sortase‐catalysed anchoring of surface proteins to the cell wall of Staphylococcus aureus
Authors: Mazmanian Sarkis K. , Ton‐That Hung , Schneewind Olaf 
Published: March 2003

Many surface proteins of Gram‐positive bacteria are anchored to the cell wall envelope by a transpeptidation mechanism, requiring a C‐terminal sorting signal with a conserved LPXTG motif. Sortase, a membrane protein of Staphylococcus aureus, cleaves polypeptides between the threonine and the glycine of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl‐group of threonine and the amino‐group of peptidoglycan cross‐bridges. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope.
PapB paralogues and their effect on the phase variation of type 1 fimbriae in Escherichia coli
Authors: Holden Nicola J. , Uhlin Bernt Eric , Gally David L. 
Published: March 2003

Recent work has demonstrated that expression of type 1 fimbriae is repressed by PapB, a regulator of pyelonephritis‐associated pili (P‐pili). PapB belongs to family of related adhesin regulators, for which consensus residues required for DNA binding and oligomerization have been identified. Of the regulators tested in this study, PapB, SfaB (S‐fimbriae) and PefB (Salmonella enterica serovar Typhimurium –plasmid‐encoded fimbriae) repressed FimB‐promoted off‐to‐on inversion of the fim switch, although complete repression was only demonstrated by PapB. DaaA, FaeB, FanA, FanB and ClpB had no effect on fim switching. In addition, only PapB stimulated FimE‐promoted on‐to‐off inversion. Deletion analysis demonstrated that this specificity resides in the carboxy terminal of the protein, and not the amino terminal, with the central region being homologous among the family members. Exchange of Leu82 and Ile83 of PapB for the equivalent residues from the DaaA protein (Phe and Gln) within the carboxy terminal virtually abolished cross‐talk activity. Whereas PapB can bind to a region around the left inverted repeat of the fim switch, DaaA and the PapB double mutant were effectively unable to bind this region. A previously characterized PapB DNA binding mutant also failed to bind to this region and failed to inhibit FimB activity at the fim switch. Thus, repression of fim expression appears unique to PapB and SfaB within E. coli and requires DNA binding involving amino acid residues located both within the homologous core and in the heterogeneous carboxy terminus. The variation in the carboxy terminus between the PapB family members explains their differential effects on fim. This mechanism of cross‐talk seems restricted to the P and S family adhesins with type 1 fimbriae and may ensure variable and sequential expression of adhesins during urinary tract infections.
Mutations in FlbD that relieve the dependency on flagellum assembly alter the temporal and spatial pattern of developmental transcription in Caulobacter crescentus
Authors: Muir Rachel E. , Gober James W. 
Published: March 2003

SummaryThe transcription factor FlbD regulates the temporal and spatial transcription of flagellar genes in the bacterium Caulobacter crescentus. Activation of FlbD requires cell cycle progression and the assembly of an early (class II) flagellum structure. In this report, we identify 20 independent gain‐of‐function mutations in flbD that relieve regulation by flagellar assembly. One of these, flbD‐1204, contained a mutation in the receiver domain (V17M) and another, flbD‐1231, in the DNA binding domain (V451G). Both of these mutations resulted in an aberrant pattern of cell cycle transcription. The presence of the FlbD‐1204 allele also resulted in a loss of swarmer‐pole‐specific transcription. These results indicate that temporal and spatial transcription is influenced by the assembly of the nascent flagellar structure. The trans‐acting positive and negative regulatory factor, FliX, couples flagellar assembly to the activation of FlbD and, as we show here, also influences temporal transcription. Furthermore, we show that FliX can suppress the activity of FlbD mutants that cannot be phosphorylated, and that FliX is required for FlbD stability, and vice versa. These results indicate that FliX may interact directly with FlbD to regulate its activity.
An investigation into the compartmentalization of the sporulation transcription factor σE in Bacillus subtilis
Authors: Fujita Masaya , Losick Richard 
Published: March 2003

SummarySporulation in Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The σE factor, which is encoded within the spoIIG operon, is a cell‐specific regulatory protein that directs gene transcription in the mother cell. σE is synthesized as an inactive proprotein pro‐σE, which is converted to the mature factor by the putative processing enzyme SpoIIGA. Processing of pro‐σE does not commence until after asymmetric division when σE is largely confined to the mother cell. Processing depends on the signalling protein SpoIIR, which delays proteolysis until after polar septation, but the mechanism by which σE is confined to the mother cell is not understood. Previous work favoured a model in which pro‐σE localizes to the mother cell face of the polar septum, such that σE would be selectively released into mother cell cytoplasm. Based on the use of green fluorescent protein (GFP) fusions, we now report that pro‐σE is distributed approximately uniformly along all membrane surfaces and is not confined to the mother‐ cell face of the septum. Rather, our results are consistent with a model in which preferential and persistent transcription of the spoIIG operon in the mother cell and degradation of σE in the forespore contribute to the selective accumulation of σE in the mother cell. Persistent transcription of spoIIG after polar septation also contributes to the proper timing of pro‐σE processing.
Are the PE‐PGRS proteins of Mycobacterium tuberculosis variable surface antigens?
Authors: Banu Sayera , Honoré Nadine , Saint‐Joanis Brigitte , Philpott Dana , Prévost Marie‐Christine , Cole Stewart T. 
Published: March 2003

Summary Mycobacterium tuberculosis H37Rv contains 67 PE‐PGRS genes, with multiple
tandem repetitive sequences, encoding closely related proteins that are exceptionally
rich in glycine and alanine. As no functional information was available, 10 of these
genes were selected and shown to be expressed in vitro by reverse transcription–polymerase
chain reaction (RT–PCR). Antibodies against five PE‐PGRS proteins, raised
in mice by DNA vaccination, detected single proteins when the same plasmid constructs
used for immunization were expressed in epithelial cells or in reticulocyte extracts,
confirming that the PE‐PGRS proteins are antigenic. As expected from the conserved
repetitive structure, the antibodies cross‐reacted with more than one PE‐PGRS protein,
suggesting that different proteins share common epitopes. PE‐PGRS proteins were detected
by West‐ern blotting in five different mycobacterial species (M. tuberculosis,
M. bovis BCG, M. smegmatis, M. marinum and M. gordonae)
and 11 clinical isolates of M. tuberculosis. Whole‐genome comparisons of M.
tuberculosis predicted allelic diversity in the PE‐PGRS family, and this was
confirmed by immunoblot studies as size variants were detected in clinical strains.
Subcellular fractionation studies and immunoelectron microscopy localized many PE‐PGRS
proteins in the cell wall and cell membrane of M. tuberculosis. The data suggest that some PE‐PGRS proteins are variable surface antigens.