bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissociation of MgSiO
3
in the Cores of Gas Giants and Terrestrial Exoplanets
Authors: Umemoto Koichiro , Wentzcovitch Renata M. , Allen Philip B.
Published: February 2006

CaIrO
3
-type MgSiO
3
is the planet-forming silicate stable at pressures and temperatures beyond those of Earth's core-mantle boundary. First-principles quasiharmonic free-energy computations show that this mineral should dissociate into CsCl-type MgO cotunnite-type SiO
2
at pressures and temperatures expected to occur in the cores of the gas giants + and in terrestrial exoplanets. At ∼10 megabars and ∼10,000 kelvin, cotunnite-type SiO
2
should have thermally activated electron carriers and thus electrical conductivity close to metallic values. Electrons will give a large contribution to thermal conductivity, and electronic damping will suppress radiative heat transport.
A Keystone Mutualism Drives Pattern in a Power Function
Authors: Vandermeer John , Perfecto Ivette
Published: February 2006

Data that can be described by a power function are ubiquitous in nature. Although there is consensus that such data frequently emerge generally from nonlinear complex systems, a variety of specific mechanisms may be responsible for creating the pattern in particular cases. Here, we report on the distribution of a scale insect (
Coccus viridis
) that is a common agricultural pest. Its distribution in an organic coffee farm in southern Mexico generally follows a power function, but there are subtle deviations from that function. We offer a biological explanation for both adherence to the power functions and associated deviations, along with supporting evidence.
Genetic Variation Affects de Novo Translocation Frequency
Authors: Kato Takema , Inagaki Hidehito , Yamada Kouji , Kogo Hiroshi , Ohye Tamae , Kowa Hiroe , Nagaoka Kayuri , Taniguchi Mariko , Emanuel Beverly S. , Kurahashi Hiroki
Published: February 2006

Translocation is one of the most frequently occurring human chromosomal aberrations. The constitutional t(11;22)(q23;q11), which is the only known recurrent non-Robertsonian translocation, represents a good model for studying translocations in humans. Here we demonstrate polymorphisms of the palindromic sequence at the t(11;22) breakpoint that affect the frequency of de novo translocations in sperm from normal males. A typical allele consists of a perfect palindrome, producing ~10-5 de novo t(11;22) translocations. Alleles with an asymmetric center do not form the t(11;22). Our data show the importance of genome sequence on chromosomal rearrangements, a class of human mutation that is thought to be random.
Nuclear Receptor Rev-erbα Is a Critical Lithium-Sensitive Component of the Circadian Clock
Authors: Yin Lei , Wang Jing , Klein Peter S. , Lazar Mitchell A.
Published: February 2006

Lithium is commonly used to treat bipolar disorder, which is associated with altered circadian rhythm. Lithium is a potent inhibitor of glycogen synthase kinase 3 (GSK3), which regulates circadian rhythm in several organisms. In experiments with cultured cells, we show here that GSK3β phosphorylates and stabilizes the orphan nuclear receptor Rev-erbα, a negative component of the circadian clock. Lithium treatment of cells leads to rapid proteasomal degradation of Rev-erbα and activation of clock gene
Bmal1
. A form of Rev-erbα that is insensitive to lithium interferes with the expression of circadian genes. Control of Rev-erbα protein stability is thus a critical component of the peripheral clock and a biological target of lithium therapy.
Causal Reasoning in Rats
Authors: Blaisdell Aaron P. , Sawa Kosuke , Leising Kenneth J. , Waldmann Michael R.
Published: February 2006

Empirical research with nonhuman primates appears to support the view that causal reasoning is a key cognitive faculty that divides humans from animals. The claim is that animals approximate causal learning using associative processes. The present results cast doubt on that conclusion. Rats made causal inferences in a basic task that taps into core features of causal reasoning without requiring complex physical knowledge. They derived predictions of the outcomes of interventions after passive observational learning of different kinds of causal models. These competencies cannot be explained by current associative theories but are consistent with causal Bayes net theories.
Activity-Dependent Regulation of MEF2 Transcription Factors Suppresses Excitatory Synapse Number
Authors: Flavell Steven W. , Cowan Christopher W. , Kim Tae-Kyung , Greer Paul L. , Lin Yingxi , Paradis Suzanne , Griffith Eric C. , Hu Linda S. , Chen Chinfei , Greenberg Michael E.
Published: February 2006

In the mammalian nervous system, neuronal activity regulates the strength and number of synapses formed. The genetic program that coordinates this process is poorly understood. We show that myocyte enhancer factor 2 (MEF2) transcription factors suppressed excitatory synapse number in a neuronal activity- and calcineurin-dependent manner as hippocampal neurons formed synapses. In response to increased neuronal activity, calcium influx into neurons induced the activation of the calcium/calmodulin-regulated phosphatase calcineurin, which dephosphorylated and activated MEF2. When activated, MEF2 promoted the transcription of a set of genes, including
arc
and
synGAP
, that restrict synapse number. These findings define an activity-dependent transcriptional program that may control synapse number during development.
A Calcium-Regulated MEF2 Sumoylation Switch Controls Postsynaptic Differentiation
Authors: Shalizi Aryaman , Gaudillière Brice , Yuan Zengqiang , Stegmüller Judith , Shirogane Takahiro , Ge Qingyuan , Tan Yi , Schulman Brenda , Harper J. Wade , Bonni Azad
Published: February 2006

Postsynaptic differentiation of dendrites is an essential step in synapse formation. We report here a requirement for the transcription factor myocyte enhancer factor 2A (MEF2A) in the morphogenesis of postsynaptic granule neuron dendritic claws in the cerebellar cortex. A transcriptional repressor form of MEF2A that is sumoylated at lysine-403 promoted dendritic claw differentiation. Activity-dependent calcium signaling induced a calcineurin-mediated dephosphorylation of MEF2A at serine-408 and, thereby, promoted a switch from sumoylation to acetylation at lysine-403, which led to inhibition of dendritic claw differentiation. Our findings define a mechanism underlying postsynaptic differentiation that may modulate activity-dependent synapse development and plasticity in the brain.
Land of the Lost
Authors: Koch Paul L.
Published: February 2006

Twilight of the Mammoths
. Ice Age Extinctions and the Rewilding of America.
By Paul S. Martin
. University of California Press, Berkeley, CA, 2005. 270 pp. $29.95, €18.95. ISBN 0-520-23141-4. Organisms and Environments.

The author interweaves the case for the "overkill" hypothesis for the extinction of the Pleistocene megafauna with an overview of his career.
When Suburbs Collide
Authors: Wolch Jennifer
Published: February 2006

Sprawl
. A Compact History.
By Robert Bruegmann
. University of Chicago Press, Chicago, 2005. 307 pp. $27.50, €17.50. ISBN 0-226-07690-3.

Taking a contrarian position, the author argues that sprawl is a logical consequence of economic growth and democracy and that it offers people many benefits.
Trapping of a Spiral-Like Intermediate of the Bacterial Cytokinetic Protein FtsZ
Authors: Michie Katherine A. , Monahan Leigh G. , Beech Peter L. , Harry Elizabeth J.
Published: February 2006

The earliest stage in bacterial cell division is the formation of a ring, composed of the tubulin-like protein FtsZ, at the division site. Tight spatial and temporal regulation of Z-ring formation is required to ensure that division occurs precisely at midcell between two replicated chromosomes. However, the mechanism of Z-ring formation and its regulation in vivo remain unresolved. Here we identify the defect of an interesting temperature-sensitive
ftsZ
mutant (
ts1
) of
Bacillus subtilis
. At the nonpermissive temperature, the mutant protein, FtsZ(Ts1), assembles into spiral-like structures between chromosomes. When shifted back down to the permissive temperature, functional Z rings form and division resumes. Our observations support a model in which Z-ring formation at the division site arises from reorganization of a long cytoskeletal spiral form of FtsZ and suggest that the FtsZ(Ts1) protein is captured as a shorter spiral-forming intermediate that is unable to complete this reorganization step. The
ts1
mutant is likely to be very valuable in revealing how FtsZ assembles into a ring and how this occurs precisely at the division site.
Differential Localization of Mre Proteins with PBP2 in
Rhodobacter sphaeroides
Authors: Slovak Peter M. , Porter Steven L. , Armitage Judith P.
Published: February 2006

In
Rhodobacter sphaeroides
, MreB, MreC, MreD, PBP2, and RodA are encoded at the same locus. The localizations of PBP2, MreB, and MreC, which have all been implicated in the synthesis of the peptidoglycan layer, were investigated under different growth conditions to gain insight into the relationships between these proteins. Immunofluorescence microscopy showed that PBP2 localized to specific sites at the midcell of elongating cells under both aerobic and photoheterotrophic conditions. Visualizing PBP2 at different stages of the cell cycle showed that in elongating cells, PBP2 was found predominately at the midcell, with asymmetric foci and bands across the cell. PBP2 remained at midcell until the start of septation, after which it moved to midcell of the daughter cells. Deconvolution and three-dimensional reconstructions suggested that PBP2 forms a partial ring at the midcell of newly divided cells and elongated cells, while in septating cells, partial PBP2 rings were present at one-quarter and three-quarter positions. Due to the diffraction limits of light microscopy, these partial rings could represent unresolved helices. Colocalization studies showed that MreC always colocalized with PBP2, while MreB colocalized with PBP2 only during elongation; during septation, MreB remained at the septation site, whereas PBP2 relocalized to the one-quarter and three-quarter positions. These results suggest that PBP2 and MreC are involved in peptidoglycan synthesis during elongation and that this occurs at specific sites close to midcell in
R. sphaeroides
.
Integration into the Phage Attachment Site,
attB
, Impairs Multicellular Differentiation in
Stigmatella aurantiaca
Authors: Müller Susanne , Shen Hui , Hofmann Diana , Schairer Hans Ulrich , Kirby John R.
Published: February 2006

Stigmatella aurantiaca
displays a complex developmental life cycle in response to starvation conditions that results in the formation of tree-like fruiting bodies capable of producing spores. The phage Mx8, first isolated from the close relative
Myxococcus xanthus
, is unable to infect
S. aurantiaca
cells and integrate into the genome. However, plasmids containing Mx8 fragments encoding the integrase and
attP
are able to integrate at the
attB
locus in the
S. aurantiaca
genome by site-specific recombination. After recombination between
attP
and
attB
, the
S. aurantiaca
cells were incapable of building normal fruiting bodies but formed clumps and fungus-like structures characteristic of intermediate stages of development displayed by the wild type. We identified two tRNA genes,
trnD
and
trnV
, encoding tRNA
Asp
and tRNA
Val
, respectively, composing an operon at the
attB
locus of
S. aurantiaca
. Integration of
attP
-containing plasmids resulted in the incorporation of the t
Mx8
terminator sequence, in addition to a short sequence of Mx8 DNA downstream of
trnD
. The integrant was unable to process the
trnD
transcript at the normal 3′ processing site and displayed a lower level of expression of the
trnVD
operon. In addition, several developmentally regulated proteins were no longer produced in mutants following insertion at the
attB
locus. We hypothesize that the integration of the t
Mx8
terminator sequence results in reduced levels of mature tRNA
Asp
and tRNA
Val
and that altered protein production during development is thereby responsible for the observed phenotype. The
trnVD
locus thus defines a new developmental checkpoint for
Stigmatella aurantiaca
.
Nla18, a Key Regulatory Protein Required for Normal Growth and Development ofMyxococcus xanthus
Authors: Diodati Michelle E. , Ossa Faisury , Caberoy Nora B. , Jose Ivy R. , Hiraiwa Wataru , Igo Michele M. , Singer Mitchell , Garza Anthony G.
Published: February 2006

NtrC-like activators regulate the transcription of a wide variety of adaptive genes in bacteria. Previously, we demonstrated that a mutation in thentrC-like activator genenla18causes defects in fruiting body development inMyxococcus xanthus. In this report, we describe the effect thatnla18inactivation has on gene expression patterns during development and vegetative growth. Gene expression innla18mutant cells is altered in the early stages of fruiting body development. Furthermore,nla18mutant cells are defective for two of the earliest events in development, production of the intracellular starvation signal ppGpp and production of A-signal. Taken together, these results indicate that the developmental program innla18mutant cells goes awry very early. Inactivation ofnla18also causes a dramatic decrease in the vegetative growth rate ofM. xanthuscells. DNA microarray analysis revealed that the vegetative expression patterns of more than 700 genes are altered innla18mutant cells. Genes coding for putative membrane and membrane-associated proteins are among the largest classes of genes whose expression is altered bynla18inactivation. This result is supported by our findings that the profiles of membrane proteins isolated from vegetativenla18mutant and wild-type cells are noticeably different. In addition to genes that code for putative membrane proteins,nla18inactivation affects the expression of many genes that are likely to be important for protein synthesis and gene regulation. Our data are consistent with a model in which Nla18 controls vegetative growth and development by activating the expression of genes involved in gene regulation, translation, and membrane structure.
A Hydrophobic Patch in the Competence-Stimulating Peptide, a Pneumococcal Competence Pheromone, Is Essential for Specificity and Biological Activity
Authors: Johnsborg Ola , Kristiansen Per Eugen , Blomqvist Trinelise , Håvarstein Leiv Sigve
Published: February 2006

Induction of competence for natural genetic transformation in
Streptococcus pneumoniae
depends on pheromone-mediated cell-cell communication and a signaling pathway consisting of the competence-stimulating peptide (CSP), its membrane-embedded histidine kinase receptor ComD, and the cognate response regulator ComE. Extensive screening of pneumococcal isolates has revealed that two major CSP variants, CSP1 and CSP2, are found in members of this species. Even though the primary structures of CSP1 and CSP2 are about 50% identical, they are highly specific for their respective receptors, ComD1 and ComD2. In the present work, we have investigated the structural basis of this specificity by determining the three-dimensional structure of CSP1 from nuclear magnetic resonance data and comparing the agonist activity of a number of CSP1/CSP2 hybrid peptides toward the ComD1 and ComD2 receptors. Our results show that upon exposure to membrane-mimicking environments, the 17-amino-acid CSP1 pheromone adopts an amphiphilic α-helical configuration stretching from residue 6 to residue 12. Furthermore, the pattern of agonist activity displayed by the various hybrid peptides revealed that hydrophobic amino acids, some of which are situated on the nonpolar side of the α-helix, strongly contribute to CSP specificity. Together, these data indicate that the identified α-helix is an important structural feature of CSP1 which is essential for effective receptor recognition under natural conditions.
Role of the
Pseudomonas aeruginosa
PlcH Tat Signal Peptide in Protein Secretion, Transcription, and Cross-Species Tat Secretion System Compatibility
Authors: Snyder Aleksandra , Vasil Adriana I. , Zajdowicz Sheryl L. , Wilson Zachary R. , Vasil Michael L.
Published: February 2006

The secretion of PlcH and its homolog PlcN of
Pseudomonas aeruginosa
through the inner membrane depends upon a functional twin arginine translocase (Tat) system and a Tat signal sequence. Conserved twin arginine (Arg) residues within the Tat signal sequence consensus motif (S/TRRxFLK) are considered essential for the secretion of Tat substrates, but some exceptions (e.g., Lys and Arg) to the twin Arg residues in this motif have been noted. The roles of all three Arg residues within the PlcH RRRTFLK consensus motif were examined. Data are presented which indicate that Arg-9 and Arg-10 are essential for PlcH secretion across the inner membrane, but the mutation of Arg-8 (e.g., to Ala or Ser) had no observable effect on the localization of PlcH. In the signal sequence of PlcH and in all of its homologs in other bacteria, there are basic amino acid residues (Arg, Lys, and Gln) immediately adjacent to the signal peptidase cleavage site (Ala-X-Ala) that are not seen in Sec-dependent signal sequences. The mutation of these basic residues to Ala caused slightly decreased levels of extracellular PlcH, but normal localization was still observed. Deletion of the entire Tat signal sequence of PlcH not only resulted in the absence of detectable extracellular PlcH activity and protein but also caused a substantial decrease in the detectable level of
plcH
mRNA. Finally, data are presented which indicate that
P. aeruginosa
PlcH exhibits cross-species compatibility with the
Escherichia coli
Tat secretion machinery, but only when the
E. coli
Tat machinery is expressed in a
P. aeruginosa
host.
Species- and Strain-Specific Control of a Complex, Flexible Regulon by
Bordetella
BvgAS
Authors: Cummings C. A. , Bootsma H. J. , Relman D. A. , Miller J. F.
Published: February 2006

The
Bordetella
master virulence regulatory system, BvgAS, controls a spectrum of gene expression states, including the virulent Bvg
+
phase, the avirulent Bvg
−
phase, and at least one Bvg-intermediate (Bvg
i
) phase. We set out to define the species- and strain-specific features of this regulon based on global gene expression profiling. Rather than functioning as a switch, Bvg controls a remarkable continuum of gene expression states, with hundreds of genes maximally expressed in intermediate phases between the Bvg
+
and Bvg
−
poles. Comparative analysis of Bvg regulation in
B. pertussis
and
B. bronchiseptica
revealed a relatively conserved Bvg
+
phase transcriptional program and identified previously uncharacterized candidate virulence factors. In contrast, control of Bvg
−
- and Bvg
i
-phase genes diverged substantially between species; regulation of metabolic, transporter, and motility loci indicated an increased capacity in
B. bronchiseptica
, compared to
B. pertussis
, for ex vivo adaptation. Strain comparisons also demonstrated variation in gene expression patterns within species. Among the genes with the greatest variability in patterns of expression, predicted promoter sequences were nearly identical. Our data suggest that the complement of transcriptional regulators is largely responsible for transcriptional diversity. In support of this hypothesis, many putative transcriptional regulators that were Bvg regulated in
B. bronchiseptica
were deleted, inactivated, or unregulated by BvgAS in
B. pertussis
. We propose the concept of a “flexible regulon.” This flexible regulon may prove to be important for pathogen evolution and the diversification of host range specificity.
Chromosomal Integration Mechanism of Infecting Mu Virion DNA
Authors: Au T. K. , Agrawal Pushpa , Harshey Rasika M.
Published: February 2006

DNA transposition is central to the propagation of temperate phage Mu. A long-standing problem in Mu biology has been the mechanism by which the linear genome of an infecting phage, which is linked at both ends to DNA acquired from a previous host, integrates into the new host chromosome. If Mu were to use its well-established cointegrate mechanism for integration (single-strand nicks at Mu ends, joined to a staggered double-strand break in the target), the flanking host sequences would remain linked to Mu; target-primed replication of the linear integrant would subsequently break the chromosome. The absence of evidence for chromosome breaks has led to speculation that infecting Mu might use a cut-and-paste mechanism, whereby Mu DNA is cut away from the flanking sequences prior to integration. In this study we have followed the fate of the flanking DNA during the time course of Mu infection. We have found that these sequences are still attached to Mu upon integration and that they disappear soon after. The data rule out a cut-and-paste mechanism and suggest that infecting Mu integrates to generate simple insertions by a variation of its established cointegrate mechanism in which, instead of a “nick, join, and replicate” pathway, it follows a “nick, join, and process” pathway. The results show similarities with human immunodeficiency virus integration and provide a unifying mechanism for development of Mu along either the lysogenic or lytic pathway.
A
Caulobacter crescentus
Extracytoplasmic Function Sigma Factor Mediating the Response to Oxidative Stress in Stationary Phase
Authors: Alvarez-Martinez Cristina E. , Baldini Regina L. , Gomes Suely L.
Published: February 2006

Alternative sigma factors of the extracytoplasmic function (ECF) subfamily are important regulators of stress responses in bacteria and have been implicated in the control of homeostasis of the extracytoplasmic compartment of the cell. This work describes the characterization of
sigF
, encoding 1 of the 13 members of this subfamily identified in
Caulobacter crescentus
. A
sigF
-null strain was obtained and shown to be severely impaired in resistance to oxidative stress, caused by hydrogen peroxide treatment, exclusively during the stationary phase. Although
sigF
mRNA levels decrease in stationary-phase cells, the amount of σ
F
protein is greatly increased at this stage, indicating a posttranscriptional control. Data obtained indicate that the FtsH protease is either directly or indirectly involved in the control of σ
F
levels, as cells lacking this enzyme present larger amounts of the sigma factor. Increased stability of σ
F
protein in stationary-phase cells of the parental strain and in exponential-phase cells of the
ftsH
-null strain is also demonstrated. Transcriptome analysis of the
sigF
-null strain led to the identification of eight genes regulated by σ
F
during the stationary phase, including
sodA
and
msrA
, which are known to be involved in oxidative stress response.
Mycobacterium tuberculosis
Cells Growing in Macrophages Are Filamentous and Deficient in FtsZ Rings
Authors: Chauhan Ashwini , Madiraju Murty V. V. S. , Fol Marek , Lofton Hava , Maloney Erin , Reynolds Robert , Rajagopalan Malini
Published: February 2006

FtsZ, a bacterial homolog of tubulin, forms a structural element called the FtsZ ring (Z ring) at the predivisional midcell site and sets up a scaffold for the assembly of other cell division proteins. The genetic aspects of FtsZ-catalyzed cell division and its assembly dynamics in
Mycobacterium tuberculosis
are unknown. Here, with an
M. tuberculosis
strain containing FtsZ
TB
tagged with green fluorescent protein as the sole source of FtsZ, we examined FtsZ structures under various growth conditions. We found that midcell Z rings are present in approximately 11% of actively growing cells, suggesting that the low frequency of Z rings is reflective of their slow growth rate. Next, we showed that SRI-3072, a reported FtsZ
TB
inhibitor, disrupted Z-ring assembly and inhibited cell division and growth of
M. tuberculosis
. We also showed that
M. tuberculosis
cells grown in macrophages are filamentous and that only a small fraction had midcell Z rings. The majority of filamentous cells contained nonring, spiral-like FtsZ structures along their entire length. The levels of FtsZ in bacteria grown in macrophages or in broth were comparable, suggesting that Z-ring formation at midcell sites was compromised during intracellular growth. Our results suggest that the intraphagosomal milieu alters the expression of
M. tuberculosis
genes affecting Z-ring formation and thereby cell division.
Identification of
Rhodospirillum rubrum
GlnB Variants That Are Altered in Their Ability To Interact with Different Targets in Response to Nitrogen Status Signals
Authors: Zhu Yu , Conrad Mary C. , Zhang Yaoping , Roberts Gary P.
Published: February 2006

In
Rhodospirillum rubrum
, NifA, the transcriptional activator for the
nif
genes, is posttranslationally activated only by the uridylylated form of GlnB, one of three P
II
homologs in the organism. We have used the yeast two-hybrid system to detect variants of GlnB that interact better with NifA than does wild-type GlnB. When examined for physiological effects in
R. rubrum
, these GlnB* variants activated NifA in the presence of NH
4
+
, which normally blocks NifA activation completely, and in the absence of GlnD, whose uridylylation of GlnB is also normally essential for NifA activation. When these variants were tested in the two-hybrid system for their interaction with NtrB, a receptor that should interact with the nonuridylylated form of GlnB, they were uniformly weaker than wild-type GlnB in that interaction. When expressed in
R. rubrum
either as single-copy integrants or on multiple-copy plasmids, these variants were also dramatically altered in terms of their ability to regulate several other receptors involved in nitrogen metabolism, including GlnE, NtrB/NtrC, and DRAT (dinitrogenase reductase ADP-ribosyl transferase)-DRAG (dinitrogenase reductase-activating glycohydrolase). The consistent pattern throughout is that these GlnB variants partially mimic the uridylylated form of wild-type GlnB, even under nitrogen-excess conditions and in strains lacking GlnD. The results suggest that the role of uridylylation of GlnB is primarily to shift the equilibrium of GlnB from a “nitrogen-sufficient” form to a “nitrogen-deficient” form, each of which interacts with different but overlapping receptor proteins in the cell. These GlnB variants apparently shift that equilibrium through direct structural changes.
Characterization of the Bifunctional Glycosyltransferase/Acyltransferase Penicillin-Binding Protein 4 of
Listeria monocytogenes
Authors: Zawadzka-Skomiał Joanna , Markiewicz Zdzislaw , Nguyen-Distèche Martine , Devreese Bart , Frère Jean-Marie , Terrak Mohammed
Published: February 2006

Multimodular penicillin-binding proteins (PBPs) are essential enzymes responsible for bacterial cell wall peptidoglycan (PG) assembly. Their glycosyltransferase activity catalyzes glycan chain elongation from lipid II substrate (undecaprenyl-pyrophosphoryl-
N
-acetylglucosamine-
N
-acetylmuramic acid-pentapeptide), and their transpeptidase activity catalyzes cross-linking between peptides carried by two adjacent glycan chains.
Listeria monocytogenes
is a food-borne pathogen which exerts its virulence through secreted and cell wall PG-associated virulence factors. This bacterium has five PBPs, including two bifunctional glycosyltransferase/transpeptidase class A PBPs, namely, PBP1 and PBP4. We have expressed and purified the latter and have shown that it binds penicillin and catalyzes in vitro glycan chain polymerization with an efficiency of 1,400 M
−1
s
−1
from
Escherichia coli
lipid II substrate. PBP4 also catalyzes the aminolysis (
d
-Ala as acceptor) and hydrolysis of the thiolester donor substrate benzoyl-Gly-thioglycolate, indicating that PBP4 possesses both transpeptidase and carboxypeptidase activities. Disruption of the gene
lmo2229
encoding PBP4 in
L. monocytogenes
EGD did not have any significant effect on growth rate, peptidoglycan composition, cell morphology, or sensitivity to β-lactam antibiotics but did increase the resistance of the mutant to moenomycin.
Transcription Profiling of the
mgrA
Regulon in
Staphylococcus aureus
Authors: Luong Thanh T. , Dunman Paul M. , Murphy Ellen , Projan Steven J. , Lee Chia Y.
Published: February 2006

MgrA has been shown to affect multiple
Staphylococcus aureus
genes involved in virulence and antibiotic resistance. To comprehensively identify the target genes regulated by
mgrA
, we employed a microarray method to analyze the transcription profiles of
S. aureus
Newman, its isogeneic
mgrA
mutant, and an MgrA-overproducing derivative. We compared genes that were differentially expressed at exponential or early stationary growth phases. Our results showed that MgrA affected an impressive number of genes, 175 of which were positively regulated and 180 of which were negatively regulated in an
mgrA
-specific manner. The target genes included all functional categories. The microarray results were validated by real-time reverse transcription-PCR quantitation of a set of selected genes from different functional categories. Our data also indicate that
mgrA
regulates virulence factors in a fashion analogous to that of the accessory gene regulatory locus (
agr
). Accordingly, exoproteins are upregulated and surface proteins are downregulated by the regulator, suggesting that
mgrA
may function in concert with
agr
. The fact that a large number of genes are regulated by
mgrA
implies that MgrA is a major global regulator in
S. aureus
.
Cloning, Expression, and Purification of Functional Sec11a and Sec11b, Type I Signal Peptidases of the Archaeon
Haloferax volcanii
Authors: Fine Amir , Irihimovitch Vered , Dahan Idit , Konrad Zvia , Eichler Jerry
Published: February 2006

Across evolution, type I signal peptidases are responsible for the cleavage of secretory signal peptides from proteins following their translocation across membranes. In
Archaea
, type I signal peptidases combine domain-specific features with traits found in either their eukaryal or bacterial counterparts. Eukaryal and bacterial type I signal peptidases differ in terms of catalytic mechanism, pharmacological profile, and oligomeric status. In this study, genes encoding Sec11a and Sec11b, two type I signal peptidases of the halophilic archaeon
Haloferax volcanii
, were cloned. Although both genes are expressed in cells grown in rich medium, gene deletion approaches suggest that Sec11b, but not Sec11a, is essential. For purification purposes, tagged versions of the protein products of both genes were expressed in transformed
Haloferax volcanii
, with Sec11a and Sec11b being fused to a cellulose-binding domain capable of interaction with cellulose in hypersaline surroundings. By employing an in vitro signal peptidase assay designed for use with high salt concentrations such as those encountered by halophilic archaea such as
Haloferax volcanii
, the signal peptide-cleaving activities of both isolated membranes and purified Sec11a and Sec11b were addressed. The results show that the two enzymes differentially cleave the assay substrate, raising the possibility that the Sec11a and Sec11b serve distinct physiological functions.
Involvement of the LlaKR2I Methylase in Expression of the AbiR Bacteriophage Defense System in
Lactococcus lactis
subsp.
lactis
biovar diacetylactis KR2
Authors: Yang Julie M. , DeUrraza Patricio J. , Matvienko Nadya , O'Sullivan Daniel J.
Published: February 2006

The native lactococcal plasmid, pKR223, from
Lactococcus lactis
subsp.
lactis
biovar diacetylactis KR2 encodes two distinct bacteriophage-resistant mechanisms, the LlaKR2I restriction and modification (R/M) system and the abortive infection (Abi) mechanism, AbiR, that impedes bacteriophage DNA replication. This study completed the characterization of AbiR, revealing that it is the first Abi system to be encoded by three genes,
abiRa
,
abiRb
, and
abiRc
, arranged in an operon and that it requires the methylase gene from the LlaKR2I R/M system. An analysis of deletion and insertion clones demonstrated that the AbiR operon was toxic in
L. lactis
without the presence of the LlaKR2I methylase, which is required to protect
L. lactis
from AbiR toxicity. The novelty of the AbiR system resides in its original gene organization and the unusual protective role of the LlaKR2I methylase. Interestingly, the AbiR genetic determinants are flanked by two IS
982
elements generating a likely transposable AbiR composite. This observation not only substantiated the novel function of the LlaKR2I methylase in the AbiR system but also illustrated the evolution of the LlaKR2I methylase toward a new and separate cellular function. This unique structure of both the LlaKR2I R/M system and the AbiR system may have contributed to the evolution of the LlaKR2I methylase toward a novel role comparable to that of the cell cycle-regulated methylases that include Dam and CcrM methylases. This new role for the LlaKR2I methylase offers a unique snapshot into the evolution of the cell cycle-regulated methylases from an existing R/M system.
Brucella abortus
Synthesizes Phosphatidylcholine from Choline Provided by the Host
Authors: Comerci Diego J. , Altabe Silvia , de Mendoza Diego , Ugalde Rodolfo A.
Published: February 2006

The
Brucella
cell envelope is characterized by the presence of phosphatidylcholine (PC), a common phospholipid in eukaryotes that is rare in prokaryotes. Studies on the composition of
Brucella abortus
2308 phospholipids revealed that the synthesis of PC depends on the presence of choline in the culture medium, suggesting that the methylation biosynthetic pathway is not functional. Phospholipid composition of
pmtA
and
pcs
mutants indicated that in
Brucella
, PC synthesis occurs exclusively via the phosphatidylcholine synthase pathway. Transformation of
Escherichia coli
with an expression vector containing the
B. abortus pcs
homologue was sufficient for PC synthesis upon induction with IPTG (isopropyl-β-
d
-thiogalactopyranoside), while no PC formation was detected when bacteria were transformed with a vector containing
pmtA.
These findings imply that
Brucella
depends on choline provided by the host cell to form PC. We could not detect any obvious associated phenotype in the PC-deficient strain under vegetative or intracellular growth conditions in macrophages. However, the
pcs
mutant strain displays a reproducible virulence defect in mice, which suggests that PC is necessary to sustain a chronic infection process.
Mutational Analysis of an Extracytoplasmic-Function Sigma Factor To Investigate Its Interactions with RNA Polymerase and DNA
Authors: Wilson Megan J. , Lamont Iain L.
Published: February 2006

The extracytoplasmic-function (ECF) family of sigma factors comprises a large group of proteins required for synthesis of a wide variety of extracytoplasmic products by bacteria. Residues important for core RNA polymerase (RNAP) binding, DNA melting, and promoter recognition have been identified in conserved regions 2 and 4.2 of primary sigma factors. Seventeen residues in region 2 and eight residues in region 4.2 of an ECF sigma factor, PvdS from
Pseudomonas aeruginosa
, were selected for alanine-scanning mutagenesis on the basis of sequence alignments with other sigma factors. Fourteen of the mutations in region 2 had a significant effect on protein function in an in vivo assay. Four proteins with alterations in regions 2.1 and 2.2 were purified as His-tagged fusions, and all showed a reduced affinity for core RNAP in vitro, consistent with a role in core binding. Region 2.3 and 2.4 mutant proteins retained the ability to bind core RNAP, but four mutants had reduced or no ability to cause core RNA polymerase to bind promoter DNA in a band-shift assay, identifying residues important for DNA binding. All mutations in region 4.2 reduced the activity of PvdS in vivo. Two of the region 4.2 mutant proteins were purified, and each showed a reduced ability to cause core RNA polymerase to bind to promoter DNA. The results show that some residues in PvdS have functions equivalent to those of corresponding residues in primary sigma factors; however, they also show that several residues not shared with primary sigma factors contribute to protein function.
A LuxR/LuxI-Type Quorum-Sensing System in a Plant Bacterium,
Mesorhizobium tianshanense
, Controls Symbiotic Nodulation
Authors: Zheng Huiming , Zhong Zengtao , Lai Xin , Chen Wen-Xin , Li Shunpeng , Zhu Jun
Published: February 2006

The ability of rhizobia to symbiotically fix nitrogen from the atmosphere when forming nodules on their plant hosts requires various signal transduction pathways. LuxR-LuxI-type quorum-sensing systems have been shown to be one of the players in a number of rhizobium species. In this study, we found that
Mesorhizobium tianshanense
, a moderate-growth
Rhizobium
that forms nodules on a number of licorice plants, produces multiple
N
-acyl homoserine lactone (AHL)-like molecules. A simple screen for AHL synthase genes using an
M. tianshanense
genomic expression library in
Escherichia coli
, coupled with a sensitive AHL detector, uncovered a LuxI-type synthase, MrtI, and a LuxR-type regulator, MrtR, in
M. tianshanense
. Deletions of the
mrtI
or
mrtR
locus completely abolished AHL production in
M. tianshanense
. Using
lacZ
transcriptional fusions, we found that expression of the quorum-sensing regulators is autoinduced, as
mrtI
gene expression requires MrtR and cognate AHLs and
mrtR
expression is dependent on AHLs. Compared with the wild-type strains, quorum-sensing-deficient mutants showed a marked reduction in the efficiency of root hair adherence and, more importantly, were defective in nodule formation on their host plant,
Glycyrrhiza uralensis
. These data provide strong evidence that quorum sensing plays a critical role in the
M. tianshanense
symbiotic process.
The Cytoplasmic C-Terminal Domain of the
Escherichia coli
KdpD Protein Functions as a K
+
Sensor
Authors: Rothenbücher Marina C. , Facey Sandra J. , Kiefer Dorothee , Kossmann Marina , Kuhn Andreas
Published: February 2006

The KdpD protein is a K
+
sensor kinase located in the cytoplasmic membrane of
Escherichia coli
. It contains four transmembrane stretches and two short periplasmic loops of 4 and 10 amino acid residues, respectively. To determine which part of KdpD functions as a K
+
sensor, genetic variants were constructed with truncations or altered arrangements of the transmembrane segments. All KdpD constructs were tested by complementation of an
E. coli kdpD
deletion strain for their ability to grow at a K
+
concentration of 0.1 mM in the medium. A soluble protein composed of the C-terminal cytoplasmic domain was able to complement the
kdpD
deletion strain. In addition, analysis of the β-galactosidase activity of an
E. coli
strain which carries a transcriptional fusion of the upstream region of the
kdpFABC
operon and a promoterless
lacZ
gene revealed that this soluble KdpD mutant responds to changes in the K
+
concentration in the extracellular medium. The results suggest that the sensing and response functions are both located in the C-terminal domain and might be modulated by the N-terminal domain as well as by membrane anchoring.
Mechanism of Growth Inhibition by Free Bile Acids in Lactobacilli and Bifidobacteria
Authors: Kurdi Peter , Kawanishi Koji , Mizutani Kanako , Yokota Atsushi
Published: February 2006

The effects of the free bile acids (FBAs) cholic acid (CA), deoxycholic acid (DCA), and chenodeoxycholic acid on the bioenergetics and growth of lactobacilli and bifidobacteria were investigated. It was found that these FBAs reduced the internal pH levels of these bacteria with rapid and stepwise kinetics and, at certain concentrations, dissipated ΔpH. The bile acid concentrations that dissipated ΔpH corresponded with the MICs for the selected bacteria. Unlike acetate, propionate, and butyrate, FBAs dissipated the transmembrane electrical potential (ΔΨ). In
Bifidobacterium breve
JCM 1192, the synthetic proton conductor pentachlorophenol (PCP) dissipated ΔpH with a slow and continuous kinetics at a much lower concentration than FBAs did, suggesting the difference in mode of action between FBAs and true proton conductors. Membrane damage assessed by the fluorescence method and a viability decrease were also observed upon exposure to CA or DCA at the MIC but not to PCP or a short-chain fatty acid mixture. Loss of potassium ion was observed at CA concentrations more than 2 mM (0.4× MIC), while leakage of other cellular components increased at CA concentrations more than 4 mM (0.8× MIC). Additionally, in experiments with membrane phospholipid vesicles extracted from
Lactobacillus salivarius
subsp.
salicinius
JCM 1044, CA and DCA at the MIC collapsed the ΔpH with concomitant leakage of intravesicular fluorescent pH probe, while they did not show proton conductance at a lower concentration range (e.g., 0.2× MIC). Taking these observations together, we conclude that FBAs at the MIC disturb membrane integrity and that this effect can lead to leakage of proton (membrane ΔpH and ΔΨ dissipation), potassium ion, and other cellular components and eventually cell death.
Genetic Variation in the
Vibrio vulnificus
Group 1 Capsular Polysaccharide Operon
Authors: Chatzidaki-Livanis Maria , Jones Melissa K. , Wright Anita C.
Published: February 2006

Vibrio vulnificus
produces human disease associated with raw-oyster consumption or wound infections, but fatalities are limited to persons with chronic underlying illness. Capsular polysaccharide (CPS) is required for virulence, and CPS expression correlates with opaque (Op) colonies that show “phase variation” to avirulent translucent (Tr) phenotypes with reduced CPS. The results discussed here confirmed homology of a
V. vulnificus
CPS locus to the group 1 CPS operon in
Escherichia coli
. However, two distinct
V. vulnificus
genotypes or alleles were associated with the operon, and they diverged at sequences encoding hypothetical proteins and also at unique, intergenic repetitive DNA elements. Phase variation was examined under conditions that promoted high-frequency transition of Op to Tr forms. Recovery of Tr isolates in these experiments showed multiple genotypes, which were designated TR1, TR2, and TR3: CPS operons of TR1 isolates were identical to the Op parent, and cells remained phase variable but expressed reduced CPS. TR2 and TR3 showed deletion mutations in one (
wzb
) or multiple genes, respectively, and deletion mutants were acapsular and locked in the Tr phase. Complementation in
trans
restored the Op phenotype in strains with the
wzb
deletion mutation. Allelic variation in repetitive elements determined the locations, rates, and extents of deletion mutations. Thus, different mechanisms are responsible for reversible phase variation in CPS expression versus genetic deletions in the CPS operon of
V. vulnificus
. Repetitive-element-mediated deletion mutations were highly conserved within the species and are likely to promote survival in estuarine environments.
Identification and Characterization of an ATP-Dependent Hexokinase with Broad Substrate Specificity from the Hyperthermophilic Archaeon
Sulfolobus tokodaii
Authors: Nishimasu Hiroshi , Fushinobu Shinya , Shoun Hirofumi , Wakagi Takayoshi
Published: February 2006

As a new member of the glucose-phosphorylating enzymes, the ATP-dependent hexokinase from the hyperthermophilic crenarchaeon
Sulfolobus tokodaii
was purified, identified, and characterized. Our results revealed that the enzyme differs from other known enzymes in primary structure and its broad substrate specificity for both phosphoryl donors and acceptors.
Effects of Streptomycin Resistance Mutations on Posttranslational Modification of Ribosomal Protein S12
Authors: Carr Jennifer F. , Hamburg Daisy-Malloy , Gregory Steven T. , Limbach Patrick A. , Dahlberg Albert E.
Published: February 2006

Ribosomal protein S12 contains a highly conserved aspartic acid residue that is posttranslationally β-methylthiolated. Using mass spectrometry, we have determined the modification states of several S12 mutants of
Thermus thermophilus
and conclude that β-methylthiolation is not a determinant of the streptomycin phenotype.
Thermal Decomposition of Li(NTO)·2H2O and Na(NTO)·H2O (NTO = Anion of 3-Nitro-1,2,4-triazol-5-one): Kinetics Derived from T-jump/FTIR Spectroscopy
Authors: Sun Yuanhua , Zhang Tonglai , Zhang Jianguo , Qiao Xiaojing , Yang Li , Zheng Hong
Published: February 2006

A "snapshot" simulation of the surface reaction zone is captured by a thin film of material heated rapidly to temperatures characteristic of the burning surface by using the T-jump/FTIR spectroscopy. The time-to-exotherm (tx) kinetics method derived from the control voltage trace of the Pt filament can be introduced to resolve the kinetics of an energetic material owing to its high sensitivity to the thermochemical reactions. The kinetic parameters of the two title compounds are determined under different pressures. The results show that Li(NTO)·2H2O and Na(NTO)·H2O (NTO = anion of 3-nitro-1,2,4-triazol-5-one) exhibit weak pressure dependence, their decomposition is dominated by the condensed phase chemistry irrespective of the pressure in the 0.1-1.1 MPa range. The values of Ea determined here are smaller than those given by a traditional non-isothermal differential scanning colorimetry (DSC) method, which might be resembled as the surface of explosion more closely and enabled the pyrolysis surface to be incorporated into models of steady and possibly unsteady combustion. The kinetics can also be successfully used to understand the behavior of the energetic material in practical combustion problems.
Demyelination in rheumatic diseases
Authors: Theodoridou A , Settas L
Published: February 2006

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterised by multifocal areas of demyelination in the white matter of the brain and spinal cord. Autoantibodies, for example antinuclear antibodies, can also be present. MS and other demyelinating processes, such as transverse myelitis and optic neuritis (which may be clinically isolated cases or be part of the clinical spectrum of MS), are sometimes difficult to differentiate from CNS involvement in systemic autoimmune diseases like systemic lupus erythematosus (SLE), antiphospholipid syndrome (APS), Sjoegren's syndrome (SS), and Adamantiades-Behcet disease (BD). An acute isolated neurological syndrome presents the biggest diagnostic problem, since it is common in MS, but can also be the only feature or first manifestation in SLE, APS, SS, and BD. Indeed, the clinical presentation and lesions evidenced by magnetic resonance imaging may be similar.
Break-Induced Replication and Recombinational Telomere Elongation in Yeast
Authors: McEachern Michael J. , Haber James E.
Published: February 2006

When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR). In budding yeasts, there are two BIR pathways, one dependent on the Rad51 recombinase protein and one Rad51 independent; these two repair processes lead to different types of survivors in cells lacking the telomerase enzyme that is required for normal telomere maintenance. Recombination at telomeres is triggered by either excessive telomere shortening or disruptions in the function of telomere-binding proteins. Telomere elongation by BIR appears to often occur through a “roll and spread” mechanism. In this process, a telomeric circle produced by recombination at a dysfunctional telomere acts as a template for a rolling circle BIR event to form an elongated telomere. Additional BIR events can then copy the elongated sequence to all other telomeres.