bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Studies and Regulatory Interactions between thephoR-phoPOperon and thephoU,mtpA, andppkGenes ofStreptomyces lividansTK24
Authors: Ghorbel Sofiane , Kormanec Jan , Artus Alexandra , Virolle Marie-Joelle 
Published: December 2005

ABSTRACTThe PhoR/PhoP two-component system ofStreptomyces lividanswas previously shown to allow the growth of the bacteria at low Piconcentrations and to negatively control antibiotic production. The present study focuses on the transcriptional analysis ofphoRandphoP, along with thephoUandmtpAgenes that are transcribed divergently from thephoRPoperon inS. lividans. The effect ofphoR,phoP,phoU, andppkmutations on transcription of these genes was examined under phosphate-replete and phosphate-limited conditions. We demonstrated thatphoRandphoPwere cotranscribed as a leaderless bicistronic transcript cleaved at discrete sites toward the 3′ end ofphoR. In addition,phoPcould also be transcribed alone from a promoter located at the 3′ end ofphoR. ThephoUandmtpAgenes, predicted to encode metal binding proteins, were shown to be transcribed as monocistronic transcripts. The expression ofphoR-phoP,phoP, andphoUwas found to be induced under conditions of Pilimitation inS. lividansTK24. This induction, requiring both PhoR and PhoP, was significantly weaker in thephoUmutant but much stronger in theppkmutant than in the parental strain. The expression ofmtpAwas also shown to be up-regulated when Piwas limiting but independently of PhoR/PhoP. The induction ofmtpAexpression was much stronger in thephoUmutant strain than in the other strains. This study revealed interesting regulatory interactions between the different genes and allowed us to propose putative roles for PhoU and MtpA in the adaptation to phosphate scarcity.
Phenotype Microarray Profiling of
Staphylococcus aureus menD
and
hemB
Mutants with the Small-Colony-Variant Phenotype
Authors: von Eiff Christof , McNamara Peter , Becker Karsten , Bates Donna , Lei Xiang-He , Ziman Michael , Bochner Barry R. , Peters Georg , Proctor Richard A. 
Published: December 2005

ABSTRACT

Standard biochemical tests have revealed that hemin and menadione auxotrophic
Staphylococcus aureus
small-colony variants (SCVs) exhibit multiple phenotypic changes. To provide a more complete analysis of the SCV phenotype, two genetically defined mutants with a stable SCV phenotype were comprehensively tested. These mutants, generated via mutations in
menD
or
hemB
that yielded menadione and hemin auxotrophs, were subjected to phenotype microarray (PM) analysis of over 1,500 phenotypes (including utilization of different carbon, nitrogen, phosphate, and sulfur sources; growth stimulation or inhibition by amino acids and other nutrients, osmolytes, and metabolic inhibitors; and susceptibility to antibiotics). Compared to parent strain COL, the
hemB
mutant was defective in utilization of a variety of carbon sources, including Krebs cycle intermediates and compounds that ultimately generate ATP via electron transport. The phenotype of the
menD
mutant was similar to that of the
hemB
mutant, but the defects in carbon metabolism were more pronounced than those seen with the
hemB
mutant. In both mutant strains, hexose phosphates and other carbohydrates that provide ATP in the absence of electron transport stimulated growth. Other phenotypes of SCV mutants, such as hypersensitivity to sodium selenite, sodium tellurite, and sodium nitrite, were also uncovered by the PM analysis. Key results of the PM analysis were confirmed in independent growth studies and by using Etest strips for susceptibility testing. PM technology is a new and efficient technology for assessing cellular phenotypes in
S. aureus
.
Identification and Characterization of a Novel Bacterial Sulfite Oxidase with No Heme Binding Domain from
Deinococcus radiodurans
Authors: D'Errico Giovanni , Di Salle Anna , La Cara Francesco , Rossi Mosè , Cannio Raffaele 
Published: December 2005

ABSTRACT

An open reading frame (
draSO
) encoding a putative sulfite oxidase (SO) was identified in the sequence of chromosome II of
Deinococcus radiodurans
; the predicted gene product showed significant amino acid sequence homology to several bacterial and eukaryotic SOs, such as the biochemically and structurally characterized enzyme from
Arabidopsis thaliana
. Cloning of the
Deinococcus
SO gene was performed by PCR amplification from the bacterial genomic DNA, and heterologous gene expression of a histidine-tagged polypeptide was obtained in a molybdopterin-overproducing strain of
Escherichia coli
. The recombinant protein was purified to homogeneity by nickel chelating affinity chromatography, and its main kinetic and chemical physical parameters were determined. Northern blot and enzyme activity analyses indicated that
draSO
gene expression is constitutive in
D. radiodurans
and that there is no increase upon exposure to thiosulfate and/or molybdenum(II).
Electron Transport in the Pathway of Acetate Conversion to Methane in the Marine Archaeon
Methanosarcina acetivorans
Authors: Li Qingbo , Li Lingyun , Rejtar Tomas , Lessner Daniel J. , Karger Barry L. , Ferry James G. 
Published: December 2005

ABSTRACT

A liquid chromatography-hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry approach was used to determine the differential abundance of proteins in acetate-grown cells compared to that of proteins in methanol-grown cells of the marine isolate
Methanosarcina acetivorans
metabolically labeled with
14
N versus
15
N. The 246 differentially abundant proteins in
M. acetivorans
were compared with the previously reported 240 differentially expressed genes of the freshwater isolate
Methanosarcina mazei
determined by transcriptional profiling of acetate-grown cells compared to methanol-grown cells. Profound differences were revealed for proteins involved in electron transport and energy conservation. Compared to methanol-grown cells, acetate-grown
M. acetivorans
synthesized greater amounts of subunits encoded in an eight-gene transcriptional unit homologous to operons encoding the ion-translocating Rnf electron transport complex previously characterized from the
Bacteria
domain. Combined with sequence and physiological analyses, these results suggest that
M. acetivorans
replaces the H
2
-evolving Ech hydrogenase complex of freshwater
Methanosarcina
species with the Rnf complex, which generates a transmembrane ion gradient for ATP synthesis. Compared to methanol-grown cells, acetate-grown
M. acetivorans
synthesized a greater abundance of proteins encoded in a seven-gene transcriptional unit annotated for the Mrp complex previously reported to function as a sodium/proton antiporter in the
Bacteria
domain. The differences reported here between
M. acetivorans
and
M. mazei
can be attributed to an adaptation of
M. acetivorans
to the marine environment.
Two-Component Systems of
Corynebacterium glutamicum
: Deletion Analysis and Involvement of the PhoS-PhoR System in the Phosphate Starvation Response
Authors: Kočan Martina , Schaffer Steffen , Ishige Takeru , Sorger-Herrmann Ulrike , Wendisch Volker F. , Bott Michael 
Published: December 2005

ABSTRACT

Corynebacterium glutamicum
contains genes for 13 two-component signal transduction systems. In order to test for their essentiality and involvement in the adaptive response to phosphate (P
i
) starvation, a set of 12 deletion mutants was constructed. One of the mutants was specifically impaired in its ability to grow under P
i
limitation, and therefore the genes lacking in this strain were named
phoS
(encoding the sensor kinase) and
phoR
(encoding the response regulator). DNA microarray analyses with the
C. glutamicum
wild type and the Δ
phoRS
mutant supported a role for the PhoRS system in the adaptation to P
i
starvation. In contrast to the wild type, the Δ
phoRS
mutant did not induce the known P
i
starvation-inducible (
psi
) genes within 1 hour after a shift from P
i
excess to P
i
limitation, except for the
pstSCAB
operon, which was still partially induced. This indicates an activator function for PhoR and the existence of at least one additional regulator of the
pst
operon. Primer extension analysis of selected
psi
genes (
pstS
,
ugpA
,
phoR
,
ushA
, and
nucH
) confirmed the microarray data and provided evidence for positive autoregulation of the
phoRS
genes.
The Iron Control Element, Acting in Positive and Negative Control of Iron-RegulatedBradyrhizobium japonicumGenes, Is a Target for the Irr Protein
Authors: Rudolph Gesine , Semini Geo , Hauser Felix , Lindemann Andrea , Friberg Markus , Hennecke Hauke , Fischer Hans-Martin 
Published: December 2005

ABSTRACTBradyrhizobium japonicum, the nitrogen-fixing soybean symbiont, possesses a heme uptake system encoded by the gene clusterhmuVUT-hmuR-exbBD-tonB. Transcription of the divergently orientedhmuTandhmuRgenes was previously found to be induced by iron limitation and to depend on a 21-bp promoter-upstream iron control element (ICE). Here, we show by deletion analysis that the full-length ICE is needed for this type of positive control. Additional genes associated with ICE-like motifs were identified in theB. japonicumgenome, of which bll6680 and blr7895 code for bacterioferritin and rubrerythrin homologs, respectively. Transcription start site mapping revealed that their ICEs directly overlap with either the −10 promoter region or the transcription initiation site, suggesting an involvement of the ICE in negative control of both genes. Consistent with this inference was the observed down-regulation of both genes under iron limitation, which in the case of bll6680 was shown to require an intact ICE motif. Using a yeast one-hybrid system, we demonstrated in vivo interaction of the iron response regulator (Irr) with all three ICEs. Moreover, specific in vitro binding of purified Irr protein to the ICE motifs of bll6680 and blr7895 was shown in electrophoretic mobility shift experiments. A genome-wide survey for iron-regulated genes with a custom-made Affymetrix gene chip revealed 17 genes to be induced and 68 to be repressed under iron-replete conditions. Remarkably, ICE-like motifs are associated with a large subset of thoseB. japonicumgenes. We propose the ICE as an importantcis-acting element inB. japonicumwhich represents the DNA-binding site for the Irr protein and, depending on its location within promoter regions, is involved in positive or negative control of the associated iron-regulated genes.
Global Phylogeny ofMycobacterium tuberculosisBased on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set
Authors: Filliol Ingrid , Motiwala Alifiya S. , Cavatore Magali , Qi Weihong , Hazbón Manzour Hernando , Bobadilla del Valle Miriam , Fyfe Janet , García-García Lourdes , Rastogi Nalin , Sola Christophe , Zozio Thierry , Guerrero Marta Inírida , León Clara Inés , Crabtree Jonathan , Angiuoli Sam , Eisenach Kathleen D. , Durmaz Riza , Joloba Moses L. , Rendón Adrian , Sifuentes-Osornio José , Ponce de León Alfredo , Cave M. Donald , Fleischmann Robert , Whittam Thomas S. , Alland David 
Published: December 2005

ABSTRACTWe analyzed a global collection ofMycobacterium tuberculosisstrains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of theM. tuberculosissamples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting thatM. tuberculosisfirst arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction ofM. tuberculosisinto these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured byGST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences ofM. tuberculosis.
Specificity of Acyl-Homoserine Lactone Synthases Examined by Mass Spectrometry
Authors: Gould Ty A. , Herman Jake , Krank Jessica , Murphy Robert C. , Churchill Mair E. A. 
Published: December 2005

ABSTRACT

Many gram-negative bacteria produce a specific set of
N
-acyl-
l
-homoserine-lactone (AHL) signaling molecules for the purpose of quorum sensing, which is a means of regulating coordinated gene expression in a cell-density-dependent manner. AHLs are produced from acylated acyl-carrier protein (acyl-ACP) and
S
-adenosyl-
l
-methionine by the AHL synthase enzyme. The appearance of specific AHLs is due in large part to the intrinsic specificity of the enzyme for subsets of acyl-ACP substrates. Structural studies of the
Pantoea stewartii
enzyme EsaI and AHL-sensitive bioassays revealed that threonine 140 in the acyl chain binding pocket directs the enzyme toward production of 3-oxo-homoserine lactones. Mass spectrometry was used to examine the range of AHL molecular species produced by AHL synthases under a variety of conditions. An AHL selective normal-phase chromatographic purification with addition of a deuterated AHL internal standard was followed by reverse-phase liquid chromatography-tandem mass spectrometry in order to obtain estimates of the relative amounts of different AHLs from biological samples. The AHLs produced by wild-type and engineered EsaI and LasI AHL synthases show that intrinsic specificity and different cellular conditions influence the production of AHLs. The threonine at position 140 in EsaI is important for the preference for 3-oxo-acyl-ACPs, but the role of the equivalent threonine in LasI is less clear. In addition, LasI expressed in
Escherichia coli
produces a high proportion of unusual AHLs with acyl chains consisting of an odd number of carbons. Furthermore, these studies offer additional methods that will be useful for surveying and quantitating AHLs from different sources.
A
Vibrio cholerae
Relaxed (
relA
) Mutant Expresses Major Virulence Factors, Exhibits Biofilm Formation and Motility, and Colonizes the Suckling Mouse Intestine
Authors: Silva Anisia J. , Benitez Jorge A. 
Published: December 2005

ABSTRACT

We have constructed a relaxed mutant of El Tor biotype
Vibrio cholerae
strain C7258 by disruption of the RelA catalytic domain. The ability of the
V. cholerae
relaxed mutant to biosynthesize guanosine tetraphosphate and pentaphosphate was severely affected; the mutant showed a reduced growth rate in minimal medium that could be reversed by the addition of Casamino Acids, and it was thermosensitive. Contrary to published findings, the new
relA
mutant still produced significant cholera toxin and toxin-coregulated pilus. The
V. cholerae relA
mutant was motile, produced normal biofilms, and colonized the suckling mouse intestine. Our data suggest that levels of basal guanosine nucleotides pppGpp and ppGpp, rather than the availability of a stringent response, could influence expression of virulence factors, depending on strain and culture conditions. Production of hemagglutinin (HA)/protease, which requires HapR, RpoS, and the cyclic AMP receptor protein, was not strongly affected. Nevertheless, overexpression of RelA protein from an isopropyl-β-
d
-thiogalactopyranoside-inducible promoter posttranscriptionally diminished production of HA/protease.
Intact Carboxysomes in a Cyanobacterial Cell Visualized by Hilbert Differential Contrast Transmission Electron Microscopy
Authors: Kaneko Yasuko , Danev Radostin , Nagayama Kuniaki , Nakamoto Hitoshi 
Published: December 2005

ABSTRACT

Carboxysomes in rapidly frozen ice-embedded whole cells of the cyanobacterium
Synechococcus
sp. strain PCC 7942 were visualized by the recently developed Hilbert differential contrast transmission electron microscope. Structural details of carboxysomes were especially clearly visualized in the ruptured cells. The novel electron microscopy exhibited the paracrystalline arrays of molecules of the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase in the carboxysomes in much better contrast than conventional transmission electron microscopy with ultrathin sections of cells. The carboxysome was surrounded by a 5- to 6-nm-thick monolayer shell which consisted of orderly arrays of globular particles.
The Quorum-Sensing Negative Regulator RsaL of
Pseudomonas aeruginosa
Binds to the
lasI
Promoter
Authors: Rampioni Giordano , Bertani Iris , Zennaro Elisabetta , Polticelli Fabio , Venturi Vittorio , Leoni Livia 
Published: December 2005

ABSTRACT

A mutation in the
rsaL
gene of
Pseudomonas aeruginosa
produces dramatically higher amounts of
N
-acyl homoserine lactone with respect to the wild type, highlighting the key role of this negative regulator in controlling quorum sensing (QS) in this opportunistic pathogen. The DNA binding site of the RsaL protein on the
rsaL-lasI
bidirectional promoter partially overlaps the binding site of the LasR protein, consistent with the hypothesis that RsaL and LasR could be in binding competition on this promoter. This is the first direct demonstration that RsaL acts as a QS negative regulator by binding to the
lasI
promoter.
AqpZ-Mediated Water Permeability in
Escherichia coli
Measured by Stopped-Flow Spectroscopy
Authors: Mallo Rachael C. , Ashby Michael T. 
Published: December 2005

ABSTRACT

We report that the water permeability of wild-type
Escherichia coli
during exponential growth is comparable to that of an
aqpZ
disruption mutant. In contrast, an increase in permeability is observed for the wild type at the onset of the stationary stage with no significant corresponding change in the permeability of the mutant.
Contribution of the Cyclic Nucleotide Phosphodiesterases PdeA and PdeB to Adaptation of
Myxococcus xanthus
Cells to Osmotic or High-Temperature Stress
Authors: Kimura Yoshio , Nakatuma Hiromi , Sato Naoko , Ohtani Mika 
Published: December 2005

ABSTRACT

A tBLASTn search of the
Myxococcus xanthus
genome database at The Institute for Genomic Research (TIGR) identified three genes (
pdeA
,
pdeB
, and
pdeC
) that encode proteins homologous to 3′,5′-cyclic nucleotide phosphodiesterase.
pdeA
,
pdeB
, and
pdeC
mutants, constructed by replacing a part of the gene with the kanamycin or tetracycline resistance gene, showed normal growth, development, and germination under nonstress conditions. However, the spores of mutants, especially the
pdeA
and
pdeB
mutants, placed under osmotic stress germinated earlier than the wild-type spores. The phenotype was the opposite of that of the receptor-type adenylyl cyclase (
cyaA
or
cyaB
) mutant. Also,
pdeA
and
pdeB
mutants were found to have impaired growth under the condition of high-temperature stress. Intracellular cyclic AMP (cAMP) levels of
pdeA
or
pdeB
mutant cells under these stressful conditions were about 1.3-fold to 2.0-fold higher than those of wild-type cells. These results suggest that PdeA and PdeB may be involved in osmotic adaptation during spore germination and temperature adaptation during vegetative growth through the regulation of cAMP levels.
RATIONAL JORDAN DECOMPOSITION OF BILINEAR FORMS
Authors: ĐOKOVIĆ DRAGOMIR Ž. , ZHAO KAIMING 
Published: December 2005

This is a continuation of our previous work on Jordan decomposition of bilinear forms over algebraically closed fields of characteristic 0. In this note, we study Jordan decomposition of bilinear forms over any field K0 of characteristic 0. Let V0 be an n-dimensional vector space over K0. Denote by [Formula: see text] the space of bilinear forms f : V0 × V0 → K0. We say that f = g + h, where f, g, [Formula: see text], is a rational Jordan decomposition of f if, after extending the field K0 to an algebraic closure K, we obtain a Jordan decomposition over K. By using the Galois group of K/K0, we prove the existence of rational Jordan decompositions and describe a method for constructing all such decompositions. Several illustrative examples of rational Jordan decompositions of bilinear forms are included. We also show how to classify the unimodular congruence classes of bilinear forms over an algebraically closed field of characteristic different from 2 and over the real field.
Sociodynamics applied to the evolution of urban and regional structures
Authors: Weidlich Wolfgang 
Published: December 2005

The article consists of two parts. In the first section the concepts of sociodynamics are briefly explained. Sociodynamics is a general modelling strategy for the quantitative description of dynamic processes in the human society. The central concepts of sociodynamics include transition rates depending on dynamic utilities and the master equation for the probability distribution over macrovariables. From it the set of nonlinear coupled differential equations for the quasi‐meanvalues of the macrovariables can be derived.In the second part this modelling strategy is applied to two “windows of perception” of the evolution of settlement structures: one model refers to the relatively fast urban evolution on the microscale and the other refers to the relatively slow regional evolution on the macroscale.The micromodel considers the urban structure as a system of sites on which different kinds of buildings (dwellings, schools, stores, service‐stations, factories…) can be erected. The step by step evolution of the city configuration is treated as a stochastic process guided by utility considerations. The sociodynamic formalization of this concept leads to equations for the evolution of the urban city configuration. Numerical simulations illustrate this urban “microdynamics”.The macromodel treats the settlement formation in a region on a more global scale. The evolution of the density of economically active populations who produce and consume goods is considered. The driving force of density changes is the spatial difference of incomes motivating the individuals to migrate to locations of optimal income. This nonlinear process leads to the self‐organisation of spatially heterogeneous population distributions forming the settlements. Their micro‐structure can thereupon be treated by the micromodel.