bluuebunny/crossref_metadata_2025_split huggingface dataset:
AStenotrophomonas maltophiliaMultilocus Sequence Typing Scheme for Inferring Population Structure
Authors: Kaiser Sabine , Biehler Klaus , Jonas Daniel 
Published: February 2009

ABSTRACTStenotrophomonas maltophiliais an opportunistic, highly resistant, and ubiquitous pathogen. Strains have been assigned to genogroups using amplified fragment length polymorphism. Hence, isolates of environmental and clinical origin predominate in different groups. A multilocus sequence typing (MLST) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. Sequence data were assigned to 54 sequence types (ST) based on seven loci. Indices of association for all isolates and clinical isolates of 2.498 and 2.562 indicated a significant linkage disequilibrium, as well as high congruence of tree topologies from different loci. Potential recombination events were detected in one-sixth of all ST. Calculation of the mean divergence between and within predicted clusters confirmed previously defined groups and revealed five additional groups. Consideration of the different ecological origins showed that 18 out of 31 respiratory tract isolates, including 12 out of 19 isolates from cystic fibrosis (CF) patients, belonged to genogroup 6. In contrast, 16 invasive strains isolated from blood cultures were distributed among nine different genogroups. Three genogroups contained isolates of strictly environmental origin that also featured high sequence distances to other genogroups, including theS. maltophiliatype strain. On the basis of this MLST scheme, isolates can be assigned to the genogroups of this species in order to further scrutinize the population structure of this species and to unravel the uneven distribution of environmental and clinical isolates obtained from infected, colonized, or CF patients.
The Dienes Phenomenon: Competition and Territoriality in Swarming
Proteus mirabilis
Authors: Budding A. E. , Ingham C. J. , Bitter W. , Vandenbroucke-Grauls C. M. , Schneeberger P. M. 
Published: February 2009

ABSTRACT

When two different strains of swarming
Proteus mirabilis
encounter one another on an agar plate, swarming ceases and a visible line of demarcation forms. This boundary region is known as the Dienes line and is associated with the formation of rounded cells. While the Dienes line appears to be the product of distinction between self and nonself, many aspects of its formation and function are unclear. In this work, we studied Dienes line formation using clinical isolates labeled with fluorescent proteins. We show that round cells in the Dienes line originate exclusively from one of the swarms involved and that these round cells have decreased viability. In this sense one of the swarms involved is dominant over the other. Close cell proximity is required for Dienes line formation, and when strains initiate swarming in close proximity, the dominant Dienes type has a significant competitive advantage. When one strain is killed by UV irradiation, a Dienes line does not form. Killing of the dominant strain limits the induction of round cells. We suggest that both strains are actively involved in boundary formation and that round cell formation is the result of a short-range killing mechanism that mediates a competitive advantage, an advantage highly specific to the swarming state. Dienes line formation has implications for the physiology of swarming and social recognition in bacteria.
Spatial Arrangement of the β-Glucoside Transporter fromEscherichia coli
Authors: Yagur-Kroll Sharon , Ido Ayelet , Amster-Choder Orna 
Published: February 2009

ABSTRACTTheEscherichia coliBglF protein, a sugar permease of the phosphoenolpyruvate-dependent phosphotransferase system (PTS), catalyzes concomitant transport and phosphorylation of β-glucosides across the cytoplasmic membrane. Despite intensive studies of PTS permeases, the mechanism that couples sugar translocation to phosphorylation and the nature of the translocation apparatus are poorly understood. Like many PTS permeases, BglF consists of a transmembrane domain, which in addition to transmembrane helices (TMs) contains a big cytoplasmic loop and two hydrophilic domains, one containing a conserved cysteine that phosphorylates the incoming sugar. We previously reported that the big hydrophilic loop, which connects TM VI to TM VII, contains regions that alternate between facing-in and facing-out states and speculated that it is involved in creating the sugar translocation channel. In the current study we used [2-(trimethylammonium)ethyl]methanethiosulfonate bromide (MTSET), a membrane-impermeative thiol-specific reagent, to identify sites that are involved in sugar transport. These sites map to the regions that border the big loop. Using cross-linking reagents that penetrate the cell, we could demonstrate spatial proximity between positions at the center of the big loop and the phosphorylation site, suggesting that the two regions come together to execute sugar phosphotransfer. Additionally, positions on opposite ends of the big loop were found to be spatially close. Cys accessibility analyses suggested that the sugar induces a change in this region. Taken together, our results demonstrate that the big loop participates in creating the sugar pathway and explain the observed coupling between translocation of PTS sugars from the periplasm to the cytoplasm and their phosphorylation.
Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in
Escherichia coli
Authors: Åberg Anna , Fernández-Vázquez Jorge , Cabrer-Panes Juan David , Sánchez Alex , Balsalobre Carlos 
Published: February 2009

ABSTRACT

The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in
Escherichia coli
. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp
0
) and/or DksA (Δ
dksA
). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksA-deficient strains, respectively, increasing to 13% of all genes in the ppGpp
0
Δ
dksA
strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in
E. coli
.
Pyruvate Kinase-Deficient
Escherichia coli
Exhibits Increased Plasmid Copy Number and Cyclic AMP Levels
Authors: Cunningham Drew S. , Liu Zhu , Domagalski Nathan , Koepsel Richard R. , Ataai Mohammad M. , Domach Michael M. 
Published: February 2009

ABSTRACT

Previously established consequences of abolishing pyruvate kinase (Pyk) activity in
Escherichia coli
during aerobic growth on glucose include reduced acetate production, elevated hexose monophosphate (HMP) pathway flux, elevated phosphoenolpyruvate carboxylase (Ppc) flux, and an increased ratio of phosphoenolpyruvate (PEP) to pyruvate. These traits inspired two hypotheses. First, the mutant (PB25) may maintain more plasmid than the wild type (JM101) by combining traits reported to facilitate plasmid DNA synthesis (i.e., decreased Pyk flux and increased HMP pathway and Ppc fluxes). Second, PB25 likely possesses a higher level of cyclic AMP (cAMP) than JM101. This is based on reports that connect elevated PEP/pyruvate ratios to phosphotransferase system signaling and adenylate cyclase activation. To test the first hypothesis, the strains were transformed with a pUC-based, high-copy-number plasmid (pGFPuv), and copy numbers were measured. PB25 exhibited a fourfold-higher copy number than JM101 when grown at 37°C. At 42°C, its plasmid content was ninefold higher than JM101 at 37°C. To test the second hypothesis, cAMP was measured, and the results confirmed it to be higher in PB25 than JM101. This elevation was not enough to elicit a strong regulatory effect, however, as indicated by the comparative expression of the pGFPuv-based reporter gene,
gfp

uv

, under the control of the cAMP-responsive
lac
promoter. The elevated cAMP in PB25 suggests that Pyk may participate in glucose catabolite repression by serving among all of the factors that tighten gene expression.
Interactions betweenBrucella suisVirB8 and Its Homolog TraJ from the Plasmid pSB102 Underline the Dynamic Nature of Type IV Secretion Systems
Authors: Bourg Gisèle , Sube Romain , O'Callaghan David , Patey Gilles 
Published: February 2009

ABSTRACTThe proteinVirB8 plays a critical role in the assembly and function of theAgrobacterium tumefaciens virBtype IV secretion system (T4SS). The structure of the periplasmic domain of bothA.tumefaciensandBrucella suisVirB8 has been determined, and site-directed mutagenesis has revealed amino acids involved in the dimerization of VirB8 and interactions with VirB4 and VirB10. We have shown previously that TraJ, the VirB8 homologue from pSB102, and the chimeric protein TraJB8, encompassing the cytoplasmic and transmembrane (TM) domains of TraJ and the periplasmic domain of VirB8, were unable to complement aB.suismutant containing an in-frame deletion of thevirB8gene. This suggested that the presence of the TraJ cytoplasmic and TM domains could block VirB8 dimerization or assembly in the inner membrane. By bacterial two-hybrid analysis, we found that VirB8, TraJ, and the chimeras can all interact to form both homo- and heterodimers. However, the presence of the TM domain of TraJ resulted in much stronger interactions in both the homo- and heterodimers. We expressed the wild-type and chimeric proteins in wild-typeB.suis. The presence of proteins carrying the TM domain of TraJ had a dominant negative effect, leading to complete loss of virulence. This suggests that the T4SS is a dynamic structure and that strong interactions block the spatial flexibility required for correct assembly and function.
Docking and Assembly of the Type II Secretion Complex of
Vibrio cholerae
Authors: Lybarger Suzanne R. , Johnson Tanya L. , Gray Miranda D. , Sikora Aleksandra E. , Sandkvist Maria 
Published: February 2009

ABSTRACT

Secretion of cholera toxin and other virulence factors from
Vibrio cholerae
is mediated by the type II secretion (T2S) apparatus, a multiprotein complex composed of both inner and outer membrane proteins. To better understand the mechanism by which the T2S complex coordinates translocation of its substrates, we are examining the protein-protein interactions of its components, encoded by the extracellular protein secretion (
eps
) genes. In this study, we took a cell biological approach, observing the dynamics of fluorescently tagged EpsC and EpsM proteins in vivo. We report that the level and context of fluorescent protein fusion expression can have a bold effect on subcellular location and that chromosomal, intraoperon expression conditions are optimal for determining the intracellular locations of fusion proteins. Fluorescently tagged, chromosomally expressed EpsC and EpsM form discrete foci along the lengths of the cells, different from the polar localization for green fluorescent protein (GFP)-EpsM previously described, as the fusions are balanced with all their interacting partner proteins within the T2S complex. Additionally, we observed that fluorescent foci in both chromosomal GFP-EpsC- and GFP-EpsM-expressing strains disperse upon deletion of
epsD
, suggesting that EpsD is critical to the localization of EpsC and EpsM and perhaps their assembly into the T2S complex.
A Conserved Gene Cluster Rules Anaerobic Oxidative Degradation of
l
-Ornithine
Authors: Fonknechten Nuria , Perret Alain , Perchat Nadia , Tricot Sabine , Lechaplais Christophe , Vallenet David , Vergne Carine , Zaparucha Anne , Le Paslier Denis , Weissenbach Jean , Salanoubat Marcel 
Published: February 2009

ABSTRACT

For the ornithine fermentation pathway, described more than 70 years ago, genetic and biochemical information are still incomplete. We present here the experimental identification of the last four missing genes of this metabolic pathway. They encode
l
-ornithine racemase, (2
R
,4
S
)-2,4-diaminopentanoate dehydrogenase, and the two subunits of 2-amino-4-ketopentanoate thiolase. While described only for the
Clostridiaceae
to date, this pathway is shown to be more widespread.
Genome Sequences of ThreeAgrobacteriumBiovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria
Authors: Slater Steven C. , Goldman Barry S. , Goodner Brad , Setubal João C. , Farrand Stephen K. , Nester Eugene W. , Burr Thomas J. , Banta Lois , Dickerman Allan W. , Paulsen Ian , Otten Leon , Suen Garret , Welch Roy , Almeida Nalvo F. , Arnold Frank , Burton Oliver T. , Du Zijin , Ewing Adam , Godsy Eric , Heisel Sara , Houmiel Kathryn L. , Jhaveri Jinal , Lu Jing , Miller Nancy M. , Norton Stacie , Chen Qiang , Phoolcharoen Waranyoo , Ohlin Victoria , Ondrusek Dan , Pride Nicole , Stricklin Shawn L. , Sun Jian , Wheeler Cathy , Wilson Lindsey , Zhu Huijun , Wood Derek W. 
Published: February 2009

ABSTRACTThe familyRhizobiaceaecontains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, manyRhizobiumandSinorhizobiumstrains are nitrogen-fixing plant mutualists, while many strains designated asAgrobacteriumare plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of theRhizobiaceaealso have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes.Agrobacteriumstrains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain,A. tumefaciensC58, has been previously sequenced. In this study, the genomes of the biovar II strainA. radiobacterK84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strainA. vitisS4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of theAlphaproteobacteriaprovides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in selectBeta- andGammaproteobacteriaspecies. Together, these results define the evolution of chromosome architecture and gene content among theRhizobiaceaeand support a generalized mechanism for second-chromosome formation among bacteria.
Staphylococcus aureus
MazF Specifically Cleaves a Pentad Sequence, UACAU, Which Is Unusually Abundant in the mRNA for Pathogenic Adhesive Factor SraP
Authors: Zhu Ling , Inoue Koichi , Yoshizumi Satoshi , Kobayashi Hiroshi , Zhang Yonglong , Ouyang Ming , Kato Fuminori , Sugai Motoyuki , Inouye Masayori 
Published: February 2009

ABSTRACT

Escherichia coli
mRNA interferases, such as MazF and ChpBK, are sequence-specific endoribonucleases encoded by toxin-antitoxin (TA) systems present in its genome. A MazF homologue in
Staphylococcus aureus
(MazF
Sa
) has been shown to inhibit cell growth when induced in
E. coli
. Here, we determined the cleavage site for MazF
Sa
with the use of phage MS2 RNA as a substrate and CspA, an RNA chaperone, which prevents the formation of secondary structures in the RNA substrate. MazF
Sa
specifically cleaves the RNA at a pentad sequence, U↓ACAU. Bioinformatics analysis revealed that this pentad sequence is significantly abundant in several genes, including the
sraP
gene in the
S. aureus
N315 strain. This gene encodes a serine-rich protein, which is known to play an important role in adhesion of the pathogen to human tissues and thus in endovascular infection. We demonstrated that the
sraP
mRNA became extremely unstable in comparison with the
ompA
mRNA only when MazF
Sa
was induced in
E. coli
. Further bioinformatics analysis indicated that the pentad sequence is also significantly abundant in the mRNAs for all the pathogenic factors in
S. aureus
. This observation suggests a possible regulatory relationship between the MazEF
Sa
TA module and the pathogenicity in
S. aureus
.
Correlations between silicic volcanic rocks of the St Mary's Islands (southwestern India) and eastern Madagascar: implications for Late Cretaceous India–Madagascar reconstructions
Authors: Melluso Leone , Sheth Hetu C. , Mahoney John J. , Morra Vincenzo , Petrone Chiara M. , Storey Michael 
Published: February 2009

Abstract:The St Mary's Islands (southwestern India) expose silicic volcanic and sub-volcanic rocks (rhyolites and granophyric dacites) emplaced contemporaneously with the Cretaceous igneous province of Madagascar, roughly 88–90 Ma ago. The St Mary's Islands rocks have phenocrysts of plagioclase, clinopyroxene, orthopyroxene and opaque oxide, moderate enrichment in the incompatible elements (e.g. Zr = 580–720 ppm, Nb = 43–53 ppm, La/Ybn= 6.9–7.2), relatively low initial87Sr/86Sr (0.7052–0.7055) and near-chondritic initial143Nd/144Nd (0.51248–0.51249). They have mineral chemical, whole-rock chemical and isotopic compositions very close to those of rhyolites exposed between Vatomandry–Ilaka and Mananjary in eastern Madagascar, and are distinctly different from rhyolites from other sectors of the Madagascan province. We therefore postulate that the St Mary's and the Vatomandry–Ilaka–Mananjary silicic rock outcrops were adjacent before the Late Cretaceous rifting that split Madagascar from India. If so, they provide a valuable tool to check and aid traditional Cretaceous India–Madagascar reconstructions based on palaeomagnetism, matching Precambrian geological features, and geometric fitting of continental shelves.Supplementary material:Mineral analyses, mass-balance calculations and locality information are available athttp://www.geolsoc.org.uk/SUP18332.
Granitic magmatism by melting of juvenile continental crust: new constraints on the source of Palaeoproterozoic granitoids in Fennoscandia from Hf isotopes in zircon
Authors: Andersen Tom , Andersson Ulf Bertil , Graham Stuart , Åberg Göran , Simonsen Siri L. 
Published: February 2009

Abstract:

Zircons from nine Palaeoproterozoic granitoid intrusions within the southern part of the Fennoscandian Shield have been studied by laser ablation inductively coupled plasma source mass spectrometry to obtain U–Pb ages (in the range 1.88–1.68 Ga) and Hf isotope compositions. Six granitoids are from the 1.85–1.65 Ga Transscandinavian Igneous Belt; during that period more than 10
6
km
3
of granitoid magma intruded the pre-existing crust. The large majority of magmatic zircons from the nine granitoids have a limited initial range,
176
Hf/
177
Hf = 0.2816–0.2818, and define an evolutionary trend given by an initial value of ε
Hf(1.88Ga)
≈ +2 ± 3 at an average
176
Lu/
177
Hf = 0.015. These data show that a geographically extensive, long-lived, relatively homogeneous, and dominant magma source resided within 2.1–1.86 Ga Svecofennian juvenile crust between 1.88 and 1.68 Ga. Zircon xenocrysts (1.91–1.98 Ga) with initial ε
Hf
= +0 to +2.5 from one of the intrusions provide additional evidence for such a long-lived crustal source of granitic magmas in central Fennoscandia. The granitoids were emplaced during a period of active mafic underplating that supplied heat to the anatectic zone in the lower–middle crust, but little or no mantle-derived Hf to the granitic magmas, in contrast to many mixed intermediate rocks.

Supplementary material:

U–Pb analyses, age calculations and Lu–Hf data are available at
http://www.geolsoc.org.uk/SUP18330
.
Orogenic versus extensional settings for regional metamorphism: Knoydartian events in the Moine Supergroup revisited
Authors: Cutts K.A. , Hand M. , Kelsey D.E. , Strachan R.A. 
Published: February 2009

Abstract:

Considerable debate exists over the tectonic regimes associated with mid-Neoproterozoic metamorphism of the Moine Supergroup, NW Scotland. Published pressure conditions imply burial to 35–40 km, a potential doubling of crustal thickness, and hence a substantial collisional event. Re-evaluation using updated thermodynamic software suggests more modest peak pressures of
c
. 7.5 kbar implying burial to
c
. 21 km. The revised
P
–
T
path has a comparatively flat clockwise evolution from early high geothermal gradient conditions. The revised
P
–
T
conditions suggest that
c
. 800 Ma crustal thickening within the Moine Supergroup was less significant than previously envisaged and possibly preceded by extension.
Abandonment of the South Penninic–Austroalpine palaeosubduction zone, Central Alps, and shift from subduction erosion to accretion: constraints from Rb/Sr geochronology
Authors: Bachmann Raik , Glodny Johannes , Oncken Onno , Seifert Wolfgang 
Published: February 2009

Abstract:

We present new age data for the evolution of the suture zone between lower plate South Penninic and upper plate Austroalpine units in the Central European Alps. Rb/Sr deformation ages for mylonitized rocks of the South Penninic palaeosubduction mélange and for deformed Austroalpine basement (Eastern Switzerland) shed light on the pre-Alpine and Alpine deformation history along the suture, as well as on synsubduction interplate mass transfer. Rb/Sr age data define two age groups. The first group reflects pre-Alpine events within the upper plate basement, with varying degree of resetting by subsequent Alpine overprints. The second group marks the waning of subduction-related deformation along the South Penninic–Austroalpine suture zone, at around 50 Ma, and termination at
c
. 47 Ma. Identical Rb/Sr ages for pervasively deformed Austroalpine and South Penninic lithologies point to tectonic erosion of the upper plate during subduction. We propose that underplating of the Middle Penninic micro-continent at
c
. 50 Ma led to the cessation of deformation within the South Penninic mélange, and shifted the zone of active deformation into the footwall. This also caused a contemporaneous upper plate surface uplift and shutoff of sedimentation in Alpine Gosau-type forearc basins.