bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape
Authors: Bacles C. F. E. , Lowe A. J. , Ennos R. A. 
Published: December 2004

AbstractSustainable forest restoration and management practices require a thorough understanding of the influence that habitat fragmentation has on the processes shaping genetic variation and its distribution in tree populations. We quantified genetic variation at isozyme markers and chloroplast DNA (cpDNA), analysed by polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) in severely fragmented populations of Sorbus aucuparia (Rosaceae) in a single catchment (Moffat) in southern Scotland. Remnants maintain surprisingly high levels of gene diversity (HE) for isozymes (HE = 0.195) and cpDNA markers (HE = 0.490). Estimates are very similar to those from non‐fragmented populations in continental Europe, even though the latter were sampled over a much larger spatial scale. Overall, no genetic bottleneck or departures from random mating were detected in the Moffat fragments. However, genetic differentiation among remnants was detected for both types of marker (isozymes Θn = 0.043, cpDNA Θc = 0.131; G‐test, P‐value < 0.001). In this self‐incompatible, insect‐pollinated, bird‐dispersed tree species, the estimated ratio of pollen flow to seed flow between fragments is close to 1 (r = 1.36). Reduced pollen‐mediated gene flow is a likely consequence of habitat fragmentation, but effective seed dispersal by birds is probably helping to maintain high levels of genetic diversity within remnants and reduce genetic differentiation between them.
Population differentiation and recombination in wheat scab populations of Gibberella zeae from the United States
Authors: Zeller Kurt A. , Bowden Robert L. , Leslie John F. 
Published: December 2004

AbstractIn limited previous studies of the Ascomycete fungus Gibberella zeae in North America, the populations examined were genetically and phenotypically diverse and could be viewed as subsamples of a larger population. Our objective in this study was to test the hypothesis that a homogeneous, randomly mating population of G. zeae is contiguous throughout the central and eastern United States across a span of several years. We analysed presence/absence alleles based on amplified fragment length polymorphisms (AFLPs) at 30 loci, 24 of which are defined genetically on a linkage map of G. zeae, from > 500 isolates in eight field populations from seven states collected during the 1998, 1999 and 2000 cropping seasons. All these strains had AFLP profiles similar to those of standard isolates of G. zeae phylogenetic lineage 7. All the populations are genetically similar, have high genotypic diversity and little or no detectable genetic disequilibrium, and show evidence of extensive interpopulation genetic exchange. Allele frequencies in some of the populations examined are not statistically different from one another, but others are. Thus, the populations examined are not mere subsamples from a single, large, randomly mating population. Geographic distance and genetic distance between populations are correlated significantly. The observed differences are relatively small, however, indicating that while genetic isolation by distance may occur, genetic exchange has occurred at a relatively high frequency among US populations of G. zeae. We think that these differences reflect the time required for the alleles to diffuse across the distances that separate them, because relatively little linkage disequilibrium is detected either in the population as a whole or in any of the individual subpopulations.
Multiple paternity in clutches of common lizard Lacerta vivipara: data from microsatellite markers
Authors: Laloi D. , Richard M. , Lecomte J. , Massot M. , Clobert J. 
Published: December 2004

AbstractThe common lizard (Lacerta vivipara) is a small live‐bearing lacertid that reproduces once a year. In order to document the poorly known mating system of this species, we present here an assessment of multiple paternity using microsatellite markers. Paternities were established within 122 clutches belonging to two wild populations from contrasted areas and to four seminatural enclosed populations. The proportion of multiply sired clutches was found to be very high (between 50.0% and 68.2%) and similar among populations, which suggests that the mating system of this species may be insensitive to environmental and population conditions.
Conditional senescence in bacteria: death of the immortals
Authors: Nyström Thomas 
Published: December 2004

SummaryLike ageing insects, worms and mammals, growth‐arrested Escherichia coli cells accumulate oxidatively damaged proteins. In the early stages of the E. coli stationary phase, this oxidation is caused by an increased production of aberrant proteins, which are especially susceptible to oxidative attack. This route of oxidation appears to elude the classical oxidative defence proteins. The failure of growth‐arrested cells fully to combat oxidative damage may also be linked to a trade‐off between proliferation activities (primarily directed by the housekeeping sigma factor, σ70) and maintenance (primarily directed by σS). This trade‐off is regulated by the alarmone ppGpp such that elevated ppGpp levels allow σS, and other alternative sigma factors, to work in concert with σ70 by shifting their relative competitiveness for RNA polymerase binding. However, even during elevated ppGpp levels and stasis, E. coli cells maintain a basal transcription of housekeeping σ70‐dependent genes, and resources are thus partly diverted from maintenance and stress defences to activities relating to proliferation. An alternative view argues for ppGpp being involved in programmed cell death upon growth arrest by regulating chromosomally located toxin–antitoxin loci. Thus, models of bacterial senescence, like those dealing with ageing in higher organisms, encompass both stochastic deterioration theories and programming theories. This review summarizes and evaluates these models.
Soluble sugar permeases of the phosphotransferase system in Escherichia coli: evidence for two physically distinct forms of the proteins in vivo
Authors: Aboulwafa Mohammad , H. Saier Milton 
Published: December 2004

SummaryThe bacterial phosphoenolpyruvate‐dependent phosphotransferase system (PTS) consists of a set of cytoplasmic energy‐coupling proteins and various integral membrane permeases/sugar phosphotransferases, each specific for a different sugar. We have conducted biochemical analyses of three PTS permeases (enzymes II), the glucose permease (IIGlc), the mannitol permease (IIMtl) and the mannose permease (IIMan). These enzymes each catalyse two vectorial/chemical reactions, sugar phosphorylation using phosphoenolpyruvate (PEP) as the phosphoryl donor, dependent on enzyme I, HPr and IIA as well as IIBC (the PEP reaction), and transphosphorylation using a sugar phosphate (glucose‐6‐P for IIGlc and IIMan; mannitol‐1‐P for IIMtl) as the phosphoryl donor, dependent only on IIBC (the TP reaction). When crude extracts of French‐pressed or osmotically shocked Escherichia coli cells are centrifuged in an ultracentrifuge at high speed, 5–20% of the enzyme II activity remains in the high‐speed supernatant, and passage through a gel filtration column gives two activity peaks, one in the void volume exhibiting high PEP‐dependent and TP activities, and a second included peak with high PEP‐dependent activity and high (IIMan), moderate (IIGlc) or negligible (IIMtl) TP activities. Both log and stationary phase cells exhibit comparable relative amounts of pelletable and soluble enzyme II activities, but long‐term exposure of cells to chloramphenicol results in selective loss of the soluble fraction with retention of much of the pelleted activity concomitant with extensive protein degradation. Short‐term exposure of cells to chloramphenicol results in increased activities in both fractions, possibly because of increased lipid association, with more activation in the soluble fraction than in the pelleted fraction. Western blot analyses show that the soluble IIGlc exhibits a subunit size of about 45 kDa, and all three soluble enzymes II elute from the gel filtration column with apparent molecular weights of 40–50 kDa. We propose that enzymes II of the PTS exist in two physically distinct forms in the E. coli cell, one tightly integrated into the membrane and one either soluble or loosely associated with the membrane. We also propose that the membrane‐integrated enzymes II are largely dimeric, whereas the soluble enzymes II, retarded during passage through a gel filtration column, are largely monomeric.
The archaeal cell cycle: current issues
Authors: Bernander Rolf 
Published: December 2004

SummaryThe recently discovered structural similarities between the archaeal Orc1/Cdc6 and bacterial DnaA initiator proteins for chromosome replication have exciting implications for cell cycle regulation. Together with current attempts to identify archaeal chromosome replication origins, the information is likely to yield fundamental insights into replication control in both archaea and eukaryotes within the near future. Several proteins that affect, or are likely to affect, chromatin structure and genome segregation in archaea have been described recently, including Sph1 and 2, ScpA and B, Sir2, Alba and Rio1p. Important insights into the properties of the MinD and FtsZ cell division proteins, and of putative cytoskeletal elements, have recently been gained in bacteria. As these proteins also are present among archaea, it is likely that the new information will also be essential for understanding archaeal genome segregation and cell division. A series of interesting cell cycle issues has been brought to light through the discovery of the novel Nanoarchaeota phylum, and these are outlined briefly. Exciting areas for extended cell cycle investigations of archaea are identified, including termination of chromosome replication, application of in situ cytological techniques for localization of cell cycle proteins and the regulatory roles of GTP‐binding proteins and small RNAs.
A C‐terminal EGF‐like domain governs BAD1 localization to the yeast surface and fungal adherence to phagocytes, but is dispensable in immune modulation and pathogenicity of Blastomyces dermatitidis
Authors: Brandhorst Tristan , Wüthrich Marcel , Finkel‐Jimenez Beatriz , Klein Bruce 
Published: December 2004

SummaryBAD1, an adhesin and immune modulator of Blastomyces dermatitidis, is an essential virulence factor that is released extracellularly before association with the yeast surface. Here, deletion of the C‐terminal EGF‐like domain profoundly affected BAD1 function, leading to non‐association with yeast, extracellular accumulation and impaired yeast adherence to macrophages. In equilibrium binding assays, ΔC‐term BAD1, lacking an EGF‐like domain, bound poorly to BAD1 null yeast, yielding a low affinity (Kd, 3 × 10−7 M versus 5 × 10−8 M) and Bmax (1.9 × 105 versus 7.9 × 105) compared with BAD1. Similar protein binding profiles were observed using chitin particles, reinforcing the notion that chitin fibrils are a receptor for BAD1, and that the EGF‐like domain is critical for BAD1 interactions with chitin on yeast. ΔC‐term strains bound poorly to macrophages, compared with parental or BAD1‐reconstituted null strains. However, ΔC‐term strains and the purified protein itself sharply suppressed tumour necrosis factor (TNF)‐α release by phagocytes in vitro and in lung in vivo, and the strains retained pathogenicity in a murine model of blastomycosis. Our results illustrate the previously undefined role of the EGF‐like domain for BAD1 localization to yeast surfaces during cell wall biogenesis. They also demonstrate that the requirements for host cell binding and immune modulation by BAD1 can be dissociated from one another, and that the former is unexpectedly dispensable in the requisite role of BAD1 in pathogenesis.
The composition, structure and stability of a group II chaperonin are temperature regulated in a hyperthermophilic archaeon
Authors: Kagawa Hiromi K. , Yaoi Takuro , Brocchieri Luciano , McMillan R. Andrew , Alton Thomas , Trent Jonathan D. 
Published: December 2004

SummaryThe hyperthermoacidophilic archaeonSulfolobus shibataecontains group II chaperonins, known as rosettasomes, which are two nine‐membered rings composed of three different 60 kDa subunits (TF55 alpha, beta and gamma). We sequenced the gene for the gamma subunit and studied the temperature‐dependent changes in alpha, beta and gamma expression, their association into rosettasomes and their phylogenetic relationships. Alpha and beta gene expression was increased by heat shock (30 min, 86°C) and decreased by cold shock (30 min, 60°C). Gamma expression was undetectable at heat shock temperatures and low at normal temperatures (75–79°C), but induced by cold shock. Polyacrylamide gel electrophoresis indicated thatin vitroalpha and beta subunits form homo‐oligomeric rosettasomes, and mixtures of alpha, beta and gamma form hetero‐oligomeric rosettasomes. Transmission electron microscopy revealed that beta homo‐oligomeric rosettasomes and all hetero‐oligomeric rosettasomes associate into filaments.In vivorosettasomes were hetero‐oligomeric with an average subunit ratio of 1α:1β:0.1γ in cultures grown at 75°C, a ratio of 1α:3β:1γ in cultures grown at 60°C and a ratio of 2α:3β:0γ after 86°C heat shock. Using differential scanning calorimetry, we determined denaturation temperatures (Tm) for alpha, beta and gamma subunits of 95.7°C, 96.7°C and 80.5°C, respectively, and observed that rosettasomes containing gamma were relatively less stable than those with alpha and/or beta only. We propose that,in vivo, the rosettasome structure is determined by the relative abundance of subunits and not by a fixed geometry. Furthermore, phylogenetic analyses indicate that archaeal chaperonin subunits underwent multiple duplication events within species (paralogy). The independent evolution of these paralogues raises the possibility that chaperonins have functionally diversified between species.
Interactions of the quorum sensing regulator QscR: interaction with itself and the other regulators of Pseudomonas aeruginosa LasR and RhlR
Authors: Ledgham Fouzia , Ventre Isabelle , Soscia Chantal , Foglino Maryline , Sturgis James N. , Lazdunski Andrée 
Published: December 2004

Summary Pseudomonas aeruginosa controls the production of many exoproteins and secondary metabolites via a hierarchical quorum sensing (QS) regulatory cascade involving the LuxR‐like proteins LasR, RhlR and their cognate signal molecules N‐(3‐oxododecanoyl)‐l‐homoserine lactone (3O‐C12‐HSL) and N‐(butanoyl)‐l‐homoserine lactone (C4‐HSL). The finding of a third LuxR‐type protein in P. aeruginosa, QscR, adds further complexity to this regulatory network. It has been shown previously that QscR represses transcription of three QS‐controlled gene clusters, phz (phenazine), hcn (hydrogen cyanide) and qsc105 (Chugani, Whiteley, Lee, D’Argenio, Manoil, and Greenberg, 2001, Proc Natl Acad Sci USA 98: 2752–2757). In this study, we identify two novel QscR targets these are lasB, encoding the extracellular elastase, and the second phenazine gene cluster, both of which are downregulated by QscR. In addition, we show that QscR synthesis is regulated by the two‐component response regulator GacA. Taking advantage of the in vivo fluorescence anisotropy technology that we have developed, we show that QscR can be found in several different types of association. Indeed, we identify QscR multimers in the absence of any acyl‐HSL, lower order QscR oligomers associated either with C4‐HSL or 3O‐C12‐HSL and QscR‐containing heterodimers with LasR or RhlR. The formation of heterodimers between QscR and LasR or RhlR, in the absence of acyl‐HSLs, is a very exciting, new result that should improve our understanding of the QscR network and its relationship to the production of P. aeruginosa virulence factors.
Genes required for mycobacterial growth defined by high density mutagenesis
Authors: Sassetti Christopher M. , Boyd Dana H. , Rubin Eric J. 
Published: December 2004

SummaryDespite over a century of research, tuberculosis remains a leading cause of infectious death worldwide. Faced with increasing rates of drug resistance, the identification of genes that are required for the growth of this organism should provide new targets for the design of antimycobacterial agents. Here, we describe the use of transposon site hybridization (TraSH) to comprehensively identify the genes required by the causative agent, Mycobacterium tuberculosis, for optimal growth. These genes include those that can be assigned to essential pathways as well as many of unknown function. The genes important for the growth of M. tuberculosis are largely conserved in the degenerate genome of the leprosy bacillus, Mycobacterium leprae, indicating that non‐essential functions have been selectively lost since this bacterium diverged from other mycobacteria. In contrast, a surprisingly high proportion of these genes lack identifiable orthologues in other bacteria, suggesting that the minimal gene set required for survival varies greatly between organisms with different evolutionary histories.
Light‐induced carotenogenesis in Myxococcus xanthus: functional characterization of the ECF sigma factor CarQ and antisigma factor CarR
Authors: Browning Douglas F. , Whitworth David E. , Hodgson David A. 
Published: December 2004

SummaryIllumination of dark‐grown Myxococcus xanthus with blue light leads to the induction of carotenoid synthesis. Central to this response is the activation of the light‐inducible promoter, PcarQRS, and the transcription of three downstream genes, carQ, carR and carS. Sequence analysis predicted that CarQ is a member of the ECF (extracytoplasmic function) subfamily of RNA polymerase sigma factors, and that CarR is an inner membrane protein. Genetic analysis strongly implied that CarR is an antisigma factor that sequesters CarQ in a transcriptionally inactive complex. Using in vitro transcription run‐off assays, we present biochemical evidence that CarQ functions as a bacterial sigma factor and is responsible for transcription initiation at PcarQRS. Similar experiments using the crtI promoter failed to implicate CarQ in direct transcription of the crtI gene. Experiments using the yeast two‐hybrid system demonstrated a protein–protein interaction betweefn CarQ and CarR, providing evidence of a CarQ–CarR complex. The yeast two‐hybrid system data also indicated that CarR is capable of oligomerization. Fractionation of M. xanthus membranes with the detergent sarkosyl showed that CarR was associated with the inner membrane. Furthermore, CarR was found to be unstable in illuminated stationary phase cells, providing a possible mechanism by which the CarR–CarQ complex is disrupted.
Archaeal chromatin and transcription
Authors: Reeve John N. 
Published: December 2004

SummaryArchaea contain a variety of sequence‐independent DNA binding proteins consistent with the evolution of several different, sometimes overlapping and exchangeable solutions to the problem of genome compaction. Some of these proteins undergo residue‐specific post‐translational lysine acetylation or methylation, hinting at analogues of the histone modifications that regulate eukaryotic chromatin structure and transcription. Archaeal transcription initiation most closely resembles the eukaryotic RNA polymerase II (RNAPII) system, but Archaea do not appear to have homologues of the multisubunit complexes that remodel eukaryotic chromatin and activate RNAPII initiation. In contrast, they have sequence‐specific regulators that repress and perhaps activate archaeal transcription by mechanisms superficially similar to the bacterial paradigm of regulating promoter binding by RNAP. Repressors compete with archaeal TATA‐box binding protein (TBP) and TFB for the TATA‐box and TFB‐recognition elements (BRE) of the archaeal promoter, or with archaeal RNAP for the site of transcription initiation. Transcript‐specific regulation by repressors binding to sites of transcript initiation is consistent with such sites having very little sequence conservation. However, most Archaea have only one TBP and/or TFB that presumably must therefore bind to similar TATA‐box and BRE sequences upstream of most genes. Repressors that function by competing with TBP and/or TFB binding must therefore also make additional contacts with transcript‐specific regulatory sites adjacent or remote from the TATA‐box/BRE region. The fate of the archaeal TBP and TFB following transcription initiation remains to be determined. Based on functional homology with their eukaryotic RNAPII‐system counterparts, archaeal TBP and possibly also TFB should remain bound to the TATA‐box/BRE region after transcription initiation. However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation.
CLNR1, the AREA/NIT2‐like global nitrogen regulator of the plant fungal pathogen Colletotrichum lindemuthianum is required for the infection cycle
Authors: Pellier Anne‐Laure , Laugé Richard , Veneault‐Fourrey Claire , Langin Thierry 
Published: December 2004

SummaryNitrogen starvation is generally assumed to be encountered by biotrophic and hemibiotrophic plant fungal pathogens at the beginning of their infection cycle. We tested whether nitrogen starvation constitutes a cue regulating genes that are required for pathogenicity of Colletotrichum lindemuthianum, a fungal pathogen of common bean. The clnr1 (C. lindemuthianumnitrogen regulator 1) gene, the areA/nit‐2 orthologue of C. lindemuthianum, was isolated. The predicted CLNR1 protein exhibits high amino acid sequence similarities with the AREA and NIT2 global fungal nitrogen regulators. Targeted clnr1– mutants are unable to use a wide array of nitrogen sources, indicating that clnr1 is the C. lindemuthianum major nitrogen regulatory gene. The clnr1– mutants are non‐pathogenic, although few anthracnose lesions seldom occur on whole plantlets. Surprisingly, cytological analysis reveals that the clnr1– mutants are not disturbed from the penetration stage until the end of the biotrophic phase, but that they are impaired during the setting up of the necrotrophic phase. Thus, through CLNR1, nitrogen starvation constitutes a cue for the regulation of genes that are compulsory for this stage of the C. lindemuthianum infection process. Additionally, clnr1– mutants complemented with the Aspergillus nidulans areA gene are fully pathogenic, indicating that areA is able to activate the C. lindemuthianum suited genes, normally under the control of clnr1.