bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect ofNeisseria meningitidisFur Mutations on Global Control of Gene Transcription
Authors: Delany Isabel , Grifantini Renata , Bartolini Erika , Rappuoli Rino , Scarlato Vincenzo
Published: March 2006

The ferric uptake regulator Fur is a well-known iron-responsive repressor of gene transcription, which is used by many bacteria to respond to the low-iron environment that pathogens encounter during infection. In this study we used comparative transcriptome analysis to define the role of the Fur protein in the global control of gene transcription and iron regulation inNeisseria meningitidis. By using the Fur-null mutant and its complemented derivative, we identified 83 genes whose transcription is controlled by Fur. We report that Fur may control differential expression of these genes by binding directly to their promoters or through indirect mechanisms. In addition, mutation of thefurgene resulted in the induction of the heat shock response, and transcription of these genes does not respond to iron limitation. Furthermore, analysis of the iron starvation stimulon in the Fur-null mutant provided evidences of iron-responsive regulation that is independent of Fur. We began to dissect the regulatory networks of Fur and the heat shock (stress) response inN. meningitidis, and the observed interlink between the two circuits is discussed.
The Antimicrobial Activity of Marinocine, Synthesized by
Marinomonas mediterranea
, Is Due to Hydrogen Peroxide Generated by Its Lysine Oxidase Activity
Authors: Lucas-Elío Patricia , Gómez Daniel , Solano Francisco , Sanchez-Amat Antonio
Published: March 2006

Marinocine is a broad-spectrum antibacterial protein synthesized by the melanogenic marine bacterium
Marinomonas mediterranea
. This work describes the basis for the antibacterial activity of marinocine and the identification of the gene coding for this protein. The antibacterial activity is inhibited under anaerobic conditions and by the presence of catalase under aerobic conditions. Marinocine is active only in culture media containing
l
-lysine. In the presence of this amino acid, marinocine generates hydrogen peroxide, which causes cell death as confirmed by the increased sensitivity to marinocine of
Escherichia coli
strains mutated in catalase activity. The gene coding for this novel enzyme was cloned using degenerate PCR with primers designed based on conserved regions in the antimicrobial protein AlpP, synthesized by
Pseudoalteromonas tunicata
, and some hypothetical proteins. The gene coding for marinocine has been named
lodA
, standing for lysine oxidase, and it seems to form part of an operon with a second gene,
lodB
, that codes for a putative dehydrogenase flavoprotein. The identity of marinocine as LodA has been demonstrated by N-terminal sequencing of purified marinocine and generation of
lodA
mutants that lose their antimicrobial activity. This is the first report on a bacterial lysine oxidase activity and the first time that a gene encoding this activity has been cloned.
Organization of FliN Subunits in the Flagellar Motor of
Escherichia coli
Authors: Paul Koushik , Blair David F.
Published: March 2006

FliN is a major constituent of the C ring in the flagellar basal body of many bacteria. It is present in >100 copies per flagellum and together with FliM and FliG forms the switch complex that functions in flagellar assembly, rotation, and clockwise-counterclockwise switching. FliN is essential for flagellar assembly and switching, but its precise functions are unknown. The C-terminal part of the protein is best conserved and most important for function; a crystal structure of this C-terminal domain of FliN from
Thermotoga maritima
revealed a saddle-shaped dimer formed mainly from β strands (P. N. Brown, M. A. A. Mathews, L. A. Joss, C. P. Hill, and D. F. Blair, J. Bacteriol.
187:
2890-2902, 2005). Equilibrium sedimentation studies showed that FliN can form stable tetramers and that a FliM
1
FliN
4
complex is also stable. Here, we have examined the organization of FliN subunits by using targeted cross-linking. Cys residues were introduced at various positions in FliN, singly or in pairs, and disulfide cross-linking was induced by oxidation. Efficient cross-linking was observed for certain positions near the ends of the dimer and for some positions in the structurally uncharacterized N-terminal domain. Certain combinations of two Cys replacements gave a high yield of cross-linked tetramer. The results support a model in which FliN is organized in doughnut-shaped tetramers, stabilized in part by contacts involving the N-terminal domain. Electron microscopic reconstructions show a bulge at the bottom of the C-ring whose size and shape are a close match for the hypothesized FliN tetramer.
Kinetic Characterization of the Monofunctional Glycosyltransferase from
Staphylococcus aureus
Authors: Terrak Mohammed , Nguyen-Distèche Martine
Published: March 2006

The glycosyltransferase (GT) module of class A penicillin-binding proteins (PBPs) and monofunctional GTs (MGTs) belong to the GT51 family in the sequence-based classification of GTs. They both possess five conserved motifs and use lipid II precursor (undecaprenyl-pyrophosphate-
N
-acetylglucosaminyl-
N
-acetylmuramoyl- pentapeptide) to synthesize the glycan chain of the bacterial wall peptidoglycan. MGTs appear to be dispensable for growth of some bacteria in vitro. However, new evidence shows that they may be essential for the infection process and development of pathogenic bacteria in their hosts. Only a small number of class A PBPs have been characterized so far, and no kinetic data are available on MGTs. In this study, we present the principal enzymatic properties of the
Staphylococcus aureus
MGT. The enzyme catalyzes glycan chain polymerization with an efficiency of ∼5,800 M
−1
s
−1
and has a pH optimum of 7.5, and its activity requires metal ions with a maximum observed in the presence of Mn
2+
. The properties of
S. aureus
MGT are distinct from those of
S. aureus
PBP2 and
Escherichia coli
MGT, but they are similar to those of
E. coli
PBP1b. We examined the role of the conserved Glu100 of
S. aureus
MGT (equivalent to the proposed catalytic Glu233 of
E. coli
PBP1b) by site-directed mutagenesis. The Glu100Gln mutation results in a drastic loss of GT activity. This shows that Glu100 is also critical for catalysis in
S. aureus
MGT and confirms that the conserved glutamate of the first motif EDXXFXX(H/N)X(G/A) is likely the key catalytic residue in the GT51 active site.
Comparative Genomic Analysis of Three Strains of
Ehrlichia ruminantium
Reveals an Active Process of Genome Size Plasticity
Authors: Frutos Roger , Viari Alain , Ferraz Conchita , Morgat Anne , Eychenié Sophie , Kandassamy Yane , Chantal Isabelle , Bensaid Albert , Coissac Eric , Vachiery Nathalie , Demaille Jacques , Martinez Dominique
Published: March 2006

Ehrlichia ruminantium
is the causative agent of heartwater, a major tick-borne disease of livestock in Africa that has been introduced in the Caribbean and is threatening to emerge and spread on the American mainland. We sequenced the complete genomes of two strains of
E. ruminantium
of differing phenotypes, strains Gardel (Erga; 1,499,920 bp), from the island of Guadeloupe, and Welgevonden (Erwe; 1,512,977 bp), originating in South Africa and maintained in Guadeloupe in a different cell environment. Comparative genomic analysis of these two strains was performed with the recently published parent strain of Erwe (Erwo) and other
Rickettsiales
(
Anaplasma
,
Wolbachia
, and
Rickettsia
spp.). Gene order is highly conserved between the
E. ruminantium
strains and with
A. marginale
. In contrast, there is very little conservation of gene order with members of the
Rickettsiaceae
. However, gene order may be locally conserved, as illustrated by the
tuf
operons. Eighteen truncated protein-encoding sequences (CDSs) differentiate Erga from Erwe
/
Erwo, whereas four other truncated CDSs differentiate Erwe from Erwo. Moreover,
E. ruminantium
displays the lowest coding ratio observed among bacteria due to unusually long intergenic regions. This is related to an active process of genome expansion/contraction targeted at tandem repeats in noncoding regions and based on the addition or removal of ca. 150-bp tandem units. This process seems to be specific to
E. ruminantium
and is not observed in the other
Rickettsiales
.
Role ofmurFin Cell Wall Biosynthesis: Isolation and Characterization of amurFConditional Mutant ofStaphylococcus aureus
Authors: Sobral R. G. , Ludovice A. M. , de Lencastre H. , Tomasz A.
Published: March 2006

TheStaphylococcus aureus murFgene was placed under the control of a promoter inducible by IPTG (isopropyl-β-d-thiogalactopyranoside). It was demonstrated thatmurFis an essential gene; it is cotranscribed withddlAand growth rate, level of beta-lactam antibiotic resistance, and rates of transcription of themecAandpbpBgenes paralleled the rates of transcription ofmurF. At suboptimal concentrations of the inducer, a UDP-linked muramyl tripeptide accumulated in the cytoplasm in parallel with the decline in the amounts of the normal pentapeptide cell wall precursor. The abnormal tripeptide component incorporated into the cell wall as a monomeric muropeptide, accompanied by a decrease in the oligomerization degree of the peptidoglycan. However, incorporation of the tripeptide into the cell wall was limited to a relatively low threshold value. Further reduction of the amounts of pentapeptide cell wall precursor caused a gradual decrease in the cellular amounts of peptidoglycan, the production of a thinner peripheral cell wall, aberrant septae, and an overall increase in the diameter of the cells. The observations suggest that the role ofmurFexceeds its primary function in peptidoglycan biosynthesis and may also be involved in the control of cell division.
Genomic Organization and Molecular Characterization of
Clostridium difficile
Bacteriophage ΦCD119
Authors: Govind Revathi , Fralick Joe A. , Rolfe Rial D.
Published: March 2006

In this study, we have isolated a temperate phage (ΦCD119) from a pathogenic
Clostridium difficile
strain and sequenced and annotated its genome. This virus has an icosahedral capsid and a contractile tail covered by a sheath and contains a double-stranded DNA genome. It belongs to the
Myoviridae
family of the tailed phages and the order
Caudovirales
. The genome was circularly permuted, with no physical ends detected by sequencing or restriction enzyme digestion analysis, and lacked a cos site. The DNA sequence of this phage consists of 53,325 bp, which carries 79 putative open reading frames (ORFs). A function could be assigned to 23 putative gene products, based upon bioinformatic analyses. The ΦCD119 genome is organized in a modular format, which includes modules for lysogeny, DNA replication, DNA packaging, structural proteins, and host cell lysis. The ΦCD119 attachment site
attP
lies in a noncoding region close to the putative integrase (
int
) gene. We have identified the phage integration site on the
C. difficile
chromosome (
attB
) located in a noncoding region just upstream of gene
gltP
, which encodes a carrier protein for glutamate and aspartate. This genetic analysis represents the first complete DNA sequence and annotation of a
C. difficile
phage.
Cross-Regulation of the
Bacillus subtilis glnRA
and
tnrA
Genes Provides Evidence for DNA Binding Site Discrimination by GlnR and TnrA
Authors: Zalieckas Jill M. , Wray Lewis V. , Fisher Susan H.
Published: March 2006

Two
Bacillus subtilis
transcriptional factors, TnrA and GlnR, regulate gene expression in response to changes in nitrogen availability. These two proteins have similar amino acid sequences in their DNA binding domains and bind to DNA sites (GlnR/TnrA sites) that have the same consensus sequence. Expression of the
tnrA
gene was found to be activated by TnrA and repressed by GlnR. Mutational analysis demonstrated that a GlnR/TnrA site which lies immediately upstream of the −35 region of the
tnrA
promoter is required for regulation of
tnrA
expression by both GlnR and TnrA. Expression of the
glnRA
operon, which contains two GlnR/TnrA binding sites (
glnRAo1
and
glnRAo2
) in its promoter region, is repressed by both GlnR and TnrA. The
glnRAo2
site, which overlaps the −35 region of the
glnRA
promoter, was shown to be required for regulation by both GlnR and TnrA, while the
glnRAo1
site which lies upstream of the −35 promoter region is only involved in GlnR-mediated regulation. Examination of TnrA binding to
tnrA
and
glnRA
promoter DNA in gel mobility shift experiments showed that TnrA bound with an equilibrium dissociation binding constant of 55 nM to the GlnR/TnrA site in the
tnrA
promoter region, while the affinities of TnrA for the two GlnR/TnrA sites in the
glnRA
promoter region were greater than 3 μM. These results demonstrate that GlnR and TnrA cross-regulate each other's expression and that there are differences in their DNA-binding specificities.
Characterization of CprK1, a CRP/FNR-Type Transcriptional Regulator of Halorespiration from
Desulfitobacterium hafniense
Authors: Gábor Krisztina , Veríssimo Carla S. , Cyran Barbara C. , ter Horst Paul , Meijer Nienke P. , Smidt Hauke , de Vos Willem M. , van der Oost John
Published: March 2006

The recently identified CprK branch of the CRP (cyclic AMP receptor protein)-FNR (fumarate and nitrate reduction regulator) family of transcriptional regulators includes proteins that activate the transcription of genes encoding proteins involved in reductive dehalogenation of chlorinated aromatic compounds. Here we report the characterization of the CprK1 protein from
Desulfitobacterium hafniense
, an anaerobic low-G+C gram-positive bacterium that is capable of reductive dechlorination of 3-chloro-4-hydroxyphenylacetic acid (Cl-OHPA). The gene encoding CprK1 was cloned and functionally overexpressed in
Escherichia coli
, and the protein was subsequently purified to homogeneity. To investigate the interaction of CprK1 with three of its predicted binding sequences (dehaloboxes), we performed in vitro DNA-binding assays (electrophoretic mobility shift assays) as well as in vivo promoter probe assays. Our results show that CprK1 binds its target dehaloboxes with high affinity (dissociation constant, 90 nM) in the presence of Cl-OHPA and that transcriptional initiation by CprK1 is influenced by deviations in the dehaloboxes from the consensus TTAAT----ATTAA sequence. A mutant CprK1 protein was created by a Val→Glu substitution at a conserved position in the recognition α-helix that gained FNR-type DNA-binding specificity, recognizing the TTGAT----ATCAA sequence (FNR box) instead of the dehaloboxes. CprK1 was subject to oxidative inactivation in vitro, most likely caused by the formation of an intermolecular disulfide bridge between Cys11 and Cys200. The possibility of redox regulation of CprK1 by a thiol-disulfide exchange reaction was investigated by using two Cys→Ser mutants. Our results indicate that a Cys11-Cys200 disulfide bridge does not appear to play a physiological role in the regulation of CprK1.
Transcriptional Analysis of the
cip-cel
Gene Cluster from
Clostridium cellulolyticum
Authors: Maamar Hédia , Abdou Laetitia , Boileau Céline , Valette Odile , Tardif Chantal
Published: March 2006

Twelve genes encoding key components of
Clostridium cellulolyticum
cellulosomes are clustered. Among them, the first, second, and fifth genes encode the assembly factor CipC and the two major cellulases Cel48F and Cel9E, respectively. Cellulolytic clones were selected from the noncellulolytic
cipC
insertional mutant
trans
-complemented with a
cipC
expression vector, in which one homologous recombination event between the 3′ end of the chromosomal
cipC
gene and the plasmidic
cipC
gene has restored the cluster continuity. The absence of the enzymes encoded by the cluster in the
cipC
mutant was thus only due to a strong polar effect, indicating that all genes were transcriptionally linked. Two large transcripts were detected in cellulose-grown cells by Northern hybridization: a 14-kb messenger which carries the
cipC-cel48F-cel8C-cel9G-cel9E
coding sequences and, in a smaller amount, a 12-kb messenger which carries the genes located in the 3′ part of the cluster. Four smaller transcripts were found in large amounts: a
cipC-cel48F
bicistronic one and three monocistronic ones,
cipC
,
cel48F
, and
cel9E
. The
cipC-cel48F
and
cel48F
messengers were shown to be stable. Analysis by reverse transcription-PCR suggested transcriptional linkage of all of the open reading frames. The production of a primary very large transcript covering the entire cluster was hypothesized. Primer extension analysis has identified two putative transcriptional start sites located 638/637 and 194 nucleotides upstream of the
cipC
translational start. The processing of the primary transcript would lead to the production of several secondary messengers displaying different stabilities, contributing to fine tuning of expression of individual genes of the operon.
Three New Regulators of Swarming inVibrio parahaemolyticus
Authors: Jaques Sandford , McCarter Linda L.
Published: March 2006

Movement on surfaces, or swarming motility, is effectively mediated by the lateral flagellar (laf) system inVibrio parahaemolyticus. Expression oflafis induced by conditions inhibiting rotation of the polar flagellum, which is used for swimming in liquid. However, not allV. parahaemolyticusisolates swarm proficiently. The organism undergoes phase variation between opaque (OP) and translucent (TR) cell types. The OP cell produces copious capsular polysaccharide and swarms poorly, whereas the TR type produces minimal capsule and swarms readily. OP↔TR switching is often the result of genetic alterations in theopaRlocus. Previously, OpaR, aVibrio harveyiLuxR homolog, was shown to activate expression of thecpsAlocus, encoding capsular polysaccharide biosynthetic genes. Here, we show that OpaR also regulates swarming by repressinglafgene expression. However, in the absence of OpaR, the swarming phenotype remains tightly surface regulated. To further investigate the genetic controls governing swarming, transposon mutagenesis of a TR (ΔopaR1) strain was performed, and SwrT, a TetR-type regulator, was identified. Loss ofswrT, a homolog ofV. harveyi luxT, created a profound defect in swarming. This defect could be rescued upon isolation of suppressor mutations that restored swarming. One class of suppressors mapped inswrZ, encoding a GntR-type transcriptional regulator. Overexpression ofswrZrepressedlafexpression. Using reporter fusions and quantitative reverse transcription-PCR, SwrT was demonstrated to repressswrZtranscription. Thus, we have identified the regulatory link that inhibits swarming of OP strains and have begun to elucidate a regulatory circuit that modulates swarming in TR strains.
Properties of Succinyl-Coenzyme A:
l
-Malate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of
Chloroflexus aurantiacus
Authors: Friedmann Silke , Steindorf Astrid , Alber Birgit E. , Fuchs Georg
Published: March 2006

The 3-hydroxypropionate cycle has been proposed to operate as the autotrophic CO
2
fixation pathway in the phototrophic bacterium
Chloroflexus aurantiacus
. In this pathway, acetyl coenzyme A (acetyl-CoA) and two bicarbonate molecules are converted to malate. Acetyl-CoA is regenerated from malyl-CoA by
l
-malyl-CoA lyase. The enzyme forming malyl-CoA, succinyl-CoA:
l
-malate coenzyme A transferase, was purified. Based on the N-terminal amino acid sequence of its two subunits, the corresponding genes were identified on a gene cluster which also contains the gene for
l
-malyl-CoA lyase, the subsequent enzyme in the pathway. Both enzymes were severalfold up-regulated under autotrophic conditions, which is in line with their proposed function in CO
2
fixation. The two CoA transferase genes were cloned and heterologously expressed in
Escherichia coli
, and the recombinant enzyme was purified and studied. Succinyl-CoA:
l
-malate CoA transferase forms a large (αβ)
n
complex consisting of 46- and 44-kDa subunits and catalyzes the reversible reaction succinyl-CoA +
l
-malate → succinate +
l
-malyl-CoA. It is specific for succinyl-CoA as the CoA donor but accepts
l
-citramalate instead of
l
-malate as the CoA acceptor; the corresponding
d
-stereoisomers are not accepted. The enzyme is a member of the class III of the CoA transferase family. The demonstration of the missing CoA transferase closes the last gap in the proposed 3-hydroxypropionate cycle.
The
Helicobacter pylori
Chemotaxis Receptor TlpB (HP0103) Is Required for pH Taxis and for Colonization of the Gastric Mucosa
Authors: Croxen Matthew A. , Sisson Gary , Melano Roberto , Hoffman Paul S.
Published: March 2006

The location of
Helicobacter pylori
in the gastric mucosa of mammals is defined by natural pH gradients within the gastric mucus, which are more alkaline proximal to the mucosal epithelial cells and more acidic toward the lumen. We have used a microscope slide-based pH gradient assay and video data collection system to document pH-tactic behavior. In response to hydrochloric acid (HCl),
H. pylori
changes its swimming pattern from straight-line random swimming to arcing or circular patterns that move the motile population away from the strong acid. Bacteria in more-alkaline regions did not swim toward the acid, suggesting the pH taxis is a form of negative chemotaxis. To identify the chemoreceptor(s) responsible for the transduction of pH-tactic signals, a vector-free allelic replacement strategy was used to construct mutations in each of the four annotated chemoreceptor genes (
tlpA
,
tlpB
,
tlpC
, and
tlpD
) in
H. pylori
strain SS1 and a motile variant of strain KE26695. All deletion mutants were motile and displayed normal chemotaxis in brucella soft agar, but only
tlpB
mutants were defective for pH taxis.
tlpD
mutants exhibited more tumbling and arcing swimming, while
tlpC
mutants were hypermotile and responsive to acid. While
tlpA
,
tlpC
, and
tlpD
mutants colonized mice to near wild-type levels,
tlpB
mutants were defective for colonization of highly permissive C57BL/6 interleukin-12 (IL-12) (p40
−/−
)-deficient mice. Complementation of the
tlpB
mutant (
tlpB
expressed from the
rdxA
locus) restored pH taxis and infectivity for mice. pH taxis, like motility and urease activity, is essential for colonization and persistence in the gastric mucosa, and thus TlpB function might represent a novel target in the development of therapeutics that blind tactic behavior.
Genes and Enzymes Involved in Caffeic Acid Biosynthesis in the Actinomycete
Saccharothrix espanaensis
Authors: Berner Martin , Krug Daniel , Bihlmaier Corina , Vente Andreas , Müller Rolf , Bechthold Andreas
Published: March 2006

The saccharomicins A and B, produced by the actinomycete
Saccharothrix espanaensis
, are oligosaccharide antibiotics. They consist of 17 monosaccharide units and the unique aglycon
N
-(
m
,
p
-dihydroxycinnamoyl)taurine. To investigate candidate genes responsible for the formation of
trans-m
,
p
-dihydroxycinnamic acid (caffeic acid) as part of the saccharomicin aglycon, gene expression experiments were carried out in
Streptomyces fradiae
XKS. It is shown that the biosynthetic pathway for
trans
-caffeic acid proceeds from
l
-tyrosine via
trans-p
-coumaric acid directly to
trans
-caffeic acid, since heterologous expression of s
am8
, encoding a tyrosine ammonia-lyase, led to the production of
trans-p
-hydroxycinnamic acid (coumaric acid), and coexpression of
sam8
and
sam5
, the latter encoding a 4-coumarate 3-hydroxylase, led to the production of
trans-m
,
p
-dihydroxycinnamic acid. This is not in accordance with the general phenylpropanoid pathway in plants, where
trans-p
-coumaric acid is first activated before the 3-hydroxylation of its ring takes place.
Control of Formation and Cellular Detachment from
Shewanella oneidensis
MR-1 Biofilms by Cyclic di-GMP
Authors: Thormann Kai M. , Duttler Stefanie , Saville Renee M. , Hyodo Mamoru , Shukla Soni , Hayakawa Yoshihiro , Spormann Alfred M.
Published: March 2006

Stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. Biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. Using
Shewanella oneidensis
MR-1, an environmentally versatile, Fe(III) and Mn(IV) mineral-reducing microorganism, we identified
mxdABCD
as a new set of genes essential for formation of a three-dimensional biofilm. Molecular analysis revealed that
mxdA
encodes a cyclic bis(3′,5′)guanylic acid (cyclic di-GMP)-forming enzyme with an unusual GGDEF motif, i.e., NVDEF, which is essential for its function.
mxdB
encodes a putative membrane-associated glycosyl transferase. Both genes are essential for matrix attachment. The attachment-deficient phenotype of a
ΔmxdA
mutant was rescued by ectopic expression of VCA0956, encoding another diguanylate cyclase. Interestingly, a rapid cellular detachment from the biofilm occurred upon induction of
yhjH
, a gene encoding an enzyme that has been shown to have phosphodiesterase activity. In this way, it was possible to bypass the previously identified sudden depletion of molecular oxygen as an environmental trigger to induce biofilm dissolution. We propose a model for c-di-GMP as a key intracellular regulator for controlling biofilm stability by shifting the state of a biofilm cell between attachment and detachment in a concentration-dependent manner.
The Intestinal Life Cycle of
Bacillus subtilis
and Close Relatives
Authors: Tam Nguyen K. M. , Uyen Nguyen Q. , Hong Huynh A. , Duc Le H. , Hoa Tran T. , Serra Claudia R. , Henriques Adriano O. , Cutting Simon M.
Published: March 2006

Bacillus subtilis
is considered a soil organism for which endospore formation provides a means to ensure long-term survival in the environment. We have addressed here the question of what happens to a spore when ingested. Spores displaying on their surface a heterologous antigen, tetanus toxin fragment C (TTFC), were shown to generate anti-TTFC responses not to the antigen contained in the primary oral inoculum but to those displayed on spores that had germinated and then resporulated. We then used reverse transcription-PCR to determine expression of vegetative genes and sporulation-specific genes in the mouse gut following oral dosing with spores. Significant levels of germination and sporulation were documented. Using natural isolates of
B. subtilis
that could form biofilms, we showed that these strains could persist in the mouse gut for significantly longer than the laboratory strain. Moreover, these isolates could grow and sporulate anaerobically and exhibited a novel phenomenon of being able to form spores in almost half the time required for the laboratory isolate. This suggests that spores are not transient passengers of the gastrointestinal tract but have adapted to carry out their entire life cycle within this environment. This is the first report showing an intestinal life cycle of
B. subtilis
and suggests that other
Bacillus
species could also be members of the gut microflora.
An Intergenic Stem-Loop Mutation in the
Bacillus subtilis ccpA-motPS
Operon Increases
motPS
Transcription and the MotPS Contribution to Motility
Authors: Terahara Naoya , Fujisawa Makoto , Powers Benjamin , Henkin Tina M. , Krulwich Terry A. , Ito Masahiro
Published: March 2006

A stem-loop mutation between
ccpA
and
motP
in the
Bacillus subtilis ccpA-motPS
operon increased
motPS
transcription and membrane-associated MotPS levels, motility, and number of flagella/cell when MotPS is the sole stator and the MotPS contribution to motility at high pH, Na
+
, and viscosity when MotAB is also present.
Analysis of the PixA Inclusion Body Protein of
Xenorhabdus nematophila
Authors: Goetsch M. , Owen H. , Goldman B. , Forst S.
Published: March 2006

The symbiotic pathogenic bacterium
Xenorhabdus nematophila
produces two distinct intracellular inclusion bodies. The
pixA
gene, which encodes the 185-residue methionine-rich PixA inclusion body protein, was analyzed in the present study. The
pixA
gene was optimally expressed under stationary-phase conditions but its expression did not require RpoS. Analysis of a
pixA
mutant strain showed that PixA was not required for virulence towards the insect host or for colonization of or survival within the nematode host, and was not essential for nematode reproduction. The
pixA
gene was not present in the genome of
Xenorhabdus bovienii
, which also produces proteinaceous inclusions, indicating that PixA is specifically produced in
X. nematophila
.
PlyPH, a Bacteriolytic Enzyme with a Broad pH Range of Activity and Lytic Action against
Bacillus anthracis
Authors: Yoong Pauline , Schuch Raymond , Nelson Daniel , Fischetti Vincent A.
Published: March 2006

We have cloned a lytic enzyme, PlyPH, with a specific lytic effect on
Bacillus anthracis
strains. PlyPH remains active between pH 4 and 10.5, and a single dose rescued a significant percentage of mice infected intraperitoneally with an attenuated
B. anthracis
strain. We propose PlyPH as a novel therapeutic agent.
Liberation of Zinc-Containing L31 (RpmE) from Ribosomes by Its Paralogous Gene Product, YtiA, inBacillus subtilis
Authors: Akanuma Genki , Nanamiya Hideaki , Natori Yousuke , Nomura Naofumi , Kawamura Fujio
Published: March 2006

We have found that alternative localization of two types of L31 ribosomal protein, RpmE and YtiA, is controlled by the intracellular concentration of zinc inBacillus subtilis. The detailed mechanisms for the alternation of L31 proteins under zinc-deficient conditions were previously unknown. To obtain further information about this regulatory mechanism, we have studied the stability of RpmE in vivo and the binding affinity of these proteins to ribosomes in vitro, and we have found that liberation of RpmE from ribosomes is triggered by the expression ofytiA, which is induced by the derepression of Zur under zinc-deficient conditions.
Microarray Analysis of the Osmotic Stress Response inPseudomonas aeruginosa
Authors: Aspedon Arden , Palmer Kelli , Whiteley Marvin
Published: March 2006

Transcriptional profiling ofPseudomonas aeruginosagrown under steady-state hyperosmotic stress conditions showed an up-regulation of genes associated with osmoprotectant synthesis, putative hydrophilins, and the type III secretion system with associated cytotoxins. A large number of regulatory genes, including several two-component systems not previously known to be influenced by osmolarity, were differentially expressed byP. aeruginosain immediate response to hyperosmotic shock.
β-Lactam Antibiotics Induce the SOS Response and Horizontal Transfer of Virulence Factors inStaphylococcus aureus
Authors: Maiques Elisa , Úbeda Carles , Campoy Susana , Salvador Noelia , Lasa Íñigo , Novick Richard P. , Barbé Jordi , Penadés José R.
Published: March 2006

Antibiotics that interfere with DNA replication and cell viability activate the SOS response. InStaphylococcus aureus, the antibiotic-induced SOS response promotes replication and high-frequency horizontal transfer of pathogenicity island-encoded virulence factors. Here we report that β-lactams induce a bona fide SOS response inS. aureus, characterized by the activation of the RecA and LexA proteins, the two master regulators of the SOS response. Moreover, we show that β-lactams are capable of triggering staphylococcal prophage induction inS. aureuslysogens. Consequently, and as previously described for SOS induction by commonly used fluoroquinolone antibiotics, β-lactam-mediated phage induction also resulted in replication and high-frequency transfer of the staphylococcal pathogenicity islands, showing that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors.
P
II
-Regulated Arginine Synthesis Controls Accumulation of Cyanophycin in
Synechocystis
sp. Strain PCC 6803
Authors: Maheswaran Mani , Ziegler Karl , Lockau Wolfgang , Hagemann Martin , Forchhammer Karl
Published: March 2006

Cyanophycin (multi-
l
-arginyl-poly-
l
-aspartic acid) is a nitrogen storage polymer found in most cyanobacteria and some heterotrophic bacteria. The cyanobacterium
Synechocystis
sp. strain PCC 6803 accumulates cyanophycin following a transition from nitrogen-limited to nitrogen-excess conditions. Here we show that the accumulation of cyanophycin depends on the activation of the key enzyme of arginine biosynthesis,
N
-acetyl-
l
-glutamate kinase, by signal transduction protein P
II
.
Altering the Length of the Lipopolysaccharide O Antigen Has an Impact on the Interaction ofSalmonella entericaSerovar Typhimurium with Macrophages and Complement
Authors: Murray Gerald L. , Attridge Stephen R. , Morona Renato
Published: March 2006

A panel of isogenicSalmonella entericaserovar Typhimurium strains that vary only in the length of the O antigen was constructed through complementation of awzzdouble mutant (displaying unregulated O-antigen length) with one of two homologous (wzzSTandwzzfepE) or three heterologous (wzzO139ofVibrio choleraeandwzzSFandwzzpHS-2ofShigella flexneri)wzzgenes. Each gene was functional in theS. entericaserovar Typhimurium host and specified production of O-antigen polymers with lengths typical of those synthesized by the donor bacteria (ranging from 2 to >100 O-antigen repeat units). By use of this panel of strains, it was found that O-antigen length influences invasion/uptake by macrophage cells; this is the first time this has been shown withSalmonella. O-antigen length was confirmed to be related to complement resistance, with a minimum protective length of >4 and <15 repeat units. O antigen of 16 to 35 repeat units was found to activate complement more efficiently than other lengths, but this was unrelated to complement resistance. No evidence was found to suggest that modifying the length of the O-antigen polymer affected expression of the O1, O4, or O5 antigenic factors.
ThecobZGene ofMethanosarcina mazeiGö1 Encodes the Nonorthologous Replacement of the α-Ribazole-5′-Phosphate Phosphatase (CobC) Enzyme ofSalmonella enterica
Authors: Zayas Carmen L. , Woodson Jesse D. , Escalante-Semerena Jorge C.
Published: March 2006

Open reading frame (ORF) Mm2058 of the methanogenic archaeonMethanosarcina mazeistrain Gö1 was shown in vivo and in vitro to encode the nonorthologous replacement of the α-ribazole-phosphate phosphatase (CobC; EC 3.1.3.73) enzyme ofSalmonella entericaserovar Typhimurium LT2. Bioinformatics analysis of sequences available in databases tentatively identified ORF Mm2058, which was cloned under the control of an inducible promoter and was used to support growth of anS. entericastrain under conditions that demanded CobC-like activity. The Mm2058 protein was expressed with a decahistidine tag at its N terminus and was purified to homogeneity using nickel affinity chromatography. High-performance liquid chromatography followed by electrospray ionization mass spectrometry showed that the Mm2058 protein had phosphatase activity that converted α-ribazole-5′-phosphate to α-ribazole, as reported for the bacterial CobC enzyme. On the basis of the data reported here, we refer to ORF Mm2058 ascobZ. We tested the prediction by Rodionov et al. (D. A. Rodionov, A. G. Vitreschak, A. A. Mironov, and M. S. Gelfand, J. Biol. Chem.278:41148-41159, 2003) that ORF HSL01294 (also called Vng1577) encoded the nonorthologous replacement of the bacterial CobC enzyme in the extremely halophilic archaeonHalobacteriumsp. strain NRC-1. A strain of the latter carrying an in-frame deletion of ORF Vng1577 was not a cobalamin auxotroph, suggesting that either there is redundancy of this function inHalobacteriumor the gene was misannotated.
BESII Results on Hadron Spectroscopy
Authors:   for the BES Collaboration., JIN Shan
Published: March 2006

In this talk, I would report the new observation of X(1835), which has properties inconsistent with any know mesons, but consistent with expectations for the state that produces the strong [Formula: see text] mass threshold enhancement observed in the [Formula: see text] process at BESII. I will also review some other multiquark candidates which are indicated by [Formula: see text] and [Formula: see text] mass threshold enhancements.
Global QCD Analysis and Hadron Collider Physics
Authors: Tung Wu-Ki
Published: March 2006

The role of global QCD analysis of parton distribution functions (PDFs) in collider physics at the Tevatron and LHC is surveyed. Current status of PDF analyses are reviewed, emphasizing the uncertainties and the open issues. The stability of NLO QCD global analysis and its prediction on "standard candle" W/Z cross sections at hadron colliders are discussed. The importance of the precise measurement of various W/Z cross sections at the Tevatron in advancing our knowledge of PDFs, hence in enhancing the capabilities of making significant progress in W mass and top quark parameter measurements, as well as the discovery potentials of Higgs and New Physics at the Tevatron and LHC, is emphasized.
QCD Effects in High Energy Processes
Authors: Li Chong Sheng , Zhu Shou-hua
Published: March 2006

In this talk, some important QCD effects in Higgs physics, supersymmetry and top physics, as well as the factorization and resummation techniques in QCD are reviewed.
HADRONIC B DECAYS WITH QCD FACTORIZATION
Authors: Beneke M.
Published: March 2006

A brief summary of outstanding theoretical issues and recent results from the QCD factorization approach to exclusive hadronic B decays is provided.
Effects of Final-State Interactions in Hadronic B Decays
Authors: Cheng Hai-Yang
Published: March 2006

Final-state rescattering effects on the hadronic B decays and their impact on direct and mixing-induced CP asymmetries are examined. Implications for some phenomenologies are briefly discussed.
THE B → ππ, πK PUZZLES: IMPLICATIONS FOR HADRON PHYSICS, NEW PHYSICS AND RARE DECAYS
Authors: FLEISCHER R.
Published: March 2006

The B-meson system is an interesting probe for the exploration of strong interactions, the quark-flavour sector of the Standard Model, and the search for new physics. In this programme, non-leptonic B decays, which are particularly challenging from the point of view of QCD, play a key rôle. After discussing strategies to deal with the corresponding hadronic matrix elements of four-quark operators and popular avenues for new physics to manifest itself in B decays, we focus on puzzling patterns in the B-factory data for B → ππ, πK decays; we explore their implications for hadron physics, new physics and rare K and B decays.
QCD Phases in Lattice QCD
Authors: AOKI SINYA
Published: March 2006

I review the recent status of lattice QCD calculations at non-zero density.
HADRONS ABOVE Tc
Authors: HATSUDA TETSUO
Published: March 2006

Hadronic modes in the quark-gluon plasma and their spectral properties are discussed on the basis of the lattice QCD data.
The Color Glass Condensate: An Intuitive Description
Authors: McLerran Larry
Published: March 2006

I argue that the physics of the scattering of very high energy strongly interacting particles is controlled by a new, universal form of matter, the Color Glass Condensate. I motivate the existence of this matter and describe some of its properties.
LATTICE QCD AND STRING THEORY
Authors: KUTI JULIUS
Published: March 2006

Bosonic string formation in gauge theories is reviewed with particular attention to the confining flux in lattice QCD and its string theory description. Recent results on the Casimir energy of the ground state and the string excitation spectrum are analyzed in the Dirichlet string limit of large separation between static sources. The closed string-soliton (torelon) with electric flux winding around a compact dimension is also discussed.
PREDICTIVE LATTICE QCD
Authors:   Fermilab Lattice, MILC, and HPQCD Collaborations., KRONFELD ANDREAS S. , ALLISON I. F. , AUBIN C. , BERNARD C. , DAVIES C. T. H. , DETAR C. , DI PIERRO M. , FREELAND E. D. , GOTTLIEB STEVEN , GRAY A. , GREGORY E. , HELLER U. M. , HETRICK J. E. , EL-KHADRA A. X. , LEVKOVA L. , MACKENZIE P. B. , MARESCA F. , MENSCHER D. , NOBES M. , OKAMOTO M. , OKTAY M. B. , OSBORN J. , RENNER D. , SIMONE J. N. , SUGAR R. , TOUSSAINT D. , TROTTIER H. D.
Published: March 2006

In the past year, we calculated with lattice QCD three quantities that were unknown or poorly known. They are the q2 dependence of the form factor in semileptonic D → Klν decay, the decay constant of the D meson, and the mass of the Bc meson. In this talk, we summarize these calculations, with emphasis on their (subsequent) confirmation by experiments.
Hadron Structure from Lattice QCD
Authors:   with LHPC collaborators., Negele J. W. , Bistrovic B. , Edwards R. G. , Fleming G. , Hägler Ph. , Orginos K. , Pochinsky A. , Renner D. B. , Richards D. G. , Schroers W.
Published: March 2006

The structure of neutrons, protons, and other strongly interacting particles is now being calculated in full, unquenched lattice QCD with quark masses entering the chiral regime. This talk describes selected examples, including the nucleon axial charge, structure functions, electromagnetic form factors, the origin of the nucleon spin, the transverse structure of the nucleon, and the nucleon to Delta transition form factor.
Hadron Spectrum from Lattice QCD
Authors: UKAWA AKIRA
Published: March 2006

A brief review is given of the lattice QCD calculation of the hadron spectrum. The status of current attempts toward inclusion of dynamical up, down and strange quarks is summarized focusing on our own work. Recent work on the possible existence of pentaquark states are assessed. We touch upon the PACS-CS Project for building our next machine for lattice QCD, and conclude with a near-term physics and machine prospects.
Review of Heavy Hadron Spectroscopy
Authors: Swanson Eric
Published: March 2006

The status of some of the recently discovered heavy hadrons is presented.
HADRON SPECTROSCOPY AND STRONG QCD
Authors: KLEMPT EBERHARD
Published: March 2006

The status of hybrids and glueballs is critically reviewed with special emphasis on the η(1440) and the ground state scalar glueball. The spectrum of baryon resonances is discussed.
CHIRAL EFFECTIVE ACTION OF QCD: PRECISION TESTS, QUESTIONS AND ELECTROWEAK EXTENSIONS
Authors: MOUSSALLAM BACHIR
Published: March 2006

This talk first discusses some aspects of the chiral expansion with three light flavours related to the (non) applicability of the OZI rule. Next, the extension of ChPT to an effective theory of the full standard model is considered. Some applications of a systematic description of the coupling constants by sum rules (e.g. to the determination of quark masses and Kl3decays) are presented.
Applications of AdS/CFT Duality to QCD
Authors: Brodsky Stanley J. , de Téramond Guy F.
Published: March 2006

Even though quantum chromodynamics is a broken conformal theory, the AdS/CFT correspondence has led to important insights into the properties of QCD. For example, as shown by Polchinski and Strassler, dimensional counting rules for the power-law falloff of hadron scattering amplitudes follow from dual holographic models with conformal behavior at short distances and confinement at large distances. We find that one also obtains a remarkable representation of the entire light-quark meson and baryon spectrum, including all orbital excitations, based on only one mass parameter. We also show how hadron light-front wavefunctions and hadron form factors in both the space-like and time-like regions can be predicted.
PROGRESS IN SMALL x RESUMMATION
Authors: FORTE STEFANO
Published: March 2006

I review recent theoretical progress in the resummation of small x contributions to the evolution of parton distributions, in view of its potential significance for accurate phenomenology at future colliders. I show that a consistent perturbative resummation of collinear and energy logs is now possible, and necessary if one wishes to use recent NNLO results in the HERA kinematic region.
NRQCD: Fundamentals and Applications to Quarkonium Decay and Production
Authors: Bodwin Geoffrey T.
Published: March 2006

I discuss NRQCD and, in particular, the NRQCD factorization formalism for quarkonium production and decay. I also summarize the current status of the comparison between the predictions of NRQCD factorization and experimental measurements.
HEAVY-QUARKONIUM PRODUCTION AT NEXT-TO-LEADING ORDER
Authors: KNIEHL BERND A.
Published: March 2006

We review recent progress in the description of heavy-quarkonium production in 2 → 2 processes at next-to-leading order in the factorization framework of nonrelativistic quantum chromodynamics. Specifically, we consider the production of prompt charmonium in association with a hadron jet or a prompt photon in two-photon collisions and exclusive double-charmonium production in e+e- annihilation.
SPECTROSCOPY OF PENTAQUARK BARYONS
Authors: OKA MAKOTO
Published: March 2006

A review is given to pentaquark mass predictions in quark models and QCD. It is pointed out that no successful quark model prediction is available for low-lying pentaquark states. Some new results of direct application of QCD, QCD sum rules and lattice QCD, are also presented.
Resolving the τ vs. Electroproduction Discrepancy for the I = 1 Vector Spectral Function and Implications for the SM Prediction for aμ
Authors: Maltman Kim
Published: March 2006

Using only independent high-scale OPE input, we investigate QCD sum rule constraints on two currently incompatible versions of the isovector vector spectral function, one obtained from electroproduction (EM) data, the other from hadronic τ decay data. Sum rules involving weighted integrals over the spectral function, from threshold to a variable upper endpoint s0, are employed. It is shown that both the normalization and slope with respect to s0 of the EM spectral integrals disagree with the corresponding OPE expectations, while both normalization and slope are in good agreement when hadronic τ decay data is used instead. These results favor determinations of the leading hadronic vacuum polarization contribution to aμ obtained using the τ decay data, and hence Standard Model predictions for aμ compatible with the current experimental determination.
Dibaryons as Carriers of Strong Internucleon Interactions and a Basis for Nuclear Physics Based on QCD
Authors: Kukulin V. I. , Pomerantsev V. N.
Published: March 2006

New concept of intermediate- and short-range nuclear force proposed by the authors a few years ago is discussed briefly. The general concept is based on an assumption on generation of the dressed dibaryon in intermediate state in NN interaction. This new mechanism has been shown to lead not only to numerous new predictions in hadronic physics but also should be responsible for a large portion of nuclear binding energy and properties of nuclear wavefunctions at high momenta.
SCALAR GLUEBALL PRODUCTION IN J/ψ HADRONIC DECAYS
Authors: Zhao Qiang , Close Frank E.
Published: March 2006

The recent data for J/ψ hadronic decays from BES raise "puzzles" about the scalar meson properties, which are different from the naive OZI rule expectation. In this work, we study the implications of a glueball-[Formula: see text] mixing scheme in the scalar meson productions in J/ψ hadronic decays. We show that the significant OZI violations in [Formula: see text] (i = 1, 2, 3 correspond to f0(1710), f0(1500) and f0(1370), respectively) are consistent with the requirement of strong glueball-[Formula: see text] mixings within the scalar meson wavefunctions.
Recent Results on Searches for Pentaquark States from STAR at RHIC
Authors:   For the STAR Collaboration., Huang Huan Zhong
Published: March 2006

We present results on pentaquark searches from nuclear collisions at RHIC with the STAR detector system. An intriguing peak has been observed in the invariant mass distribution of [Formula: see text] from 18.6 Million d + Au collision events at [Formula: see text]. The peak centers at a mass 1528 ± 2 ± 5 MeV/c 2 and the FWHM ~15 MeV/c2 limited by detector responses. The statistical significance of the peak is 4.2σ. Such a state if confirmed is manifestly exotic and implies a family of isospin one states. A weak signal of less statistical significance (~3σ) has been observed in 5.6M Au + Au collision events at 62.4 GeV. Searches in 10.7M Au + Au collision events at 200 GeV yield no significant signal. The Au + Au results neither confirm nor rule out the d + Au observation as a possible state.