bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Normal Holonomy Group of Kähler Submanifolds
Authors: Alekseevsky Dmitri V. , Di Scala Antonio J. 
Published: June 2004

We study the (restricted) holonomy group Hol(∇⊥) of the normal connection ∇⊥ (shortened to normal holonomy group) of a Kähler submanifold of a complex space form. We prove that if the normal holonomy group acts irreducibly on the normal space then it is linear isomorphic to the holonomy group of an irreducible Hermitian symmetric space. In particular, it is a compact group and the complex structure J belongs to its Lie algebra.We prove that the normal holonomy group acts irreducibly if the submanifold is full (that is, it is not contained in a totally geodesic proper Kähler submanifold) and the second fundamental form at some point has no kernel. For example, a Kähler–Einstein submanifold of CPn has this property.We define a new invariant μ of a Kähler submanifold of a complex space form. For non‐full submanifolds, the invariant μ measures the deviation of J from belonging to the normal holonomy algebra. For a Kähler–Einstein submanifold, the invariant μ is a rational function of the Einstein constant. By using the invariant μ, we prove that the normal holonomy group of a not necessarily full Kähler–Einstein submanifold of CPn is compact, and we give a list of possible holonomy groups.The approach is based on a definition of the holonomy algebra hol(P) of an arbitrary curvature tensor field P on a vector bundle with a connection and on a De Rham type decomposition theorem for hol(P). 2000 Mathematics Subject Classification 53C40 (primary), 53B25 (secondary).
Two Genetic Loci Produce Distinct Carbohydrate-Rich Structural Components of thePseudomonas aeruginosaBiofilm Matrix
Authors: Friedman Lisa , Kolter Roberto 
Published: July 2004

ABSTRACTPseudomonas aeruginosaforms biofilms, which are cellular aggregates encased in an extracellular matrix. Molecular genetics studies of three common autoaggregative phenotypes, namely wrinkled colonies, pellicles, and solid-surface-associated biofilms, led to the identification of two loci,pelandpsl, that are involved in the production of carbohydrate-rich components of the biofilm matrix. Thepelgene cluster is involved in the production of a glucose-rich matrix material inP. aeruginosastrain PA14 (L. Friedman and R. Kolter, Mol. Microbiol.51:675-690, 2004). Here we investigate the role of thepelgene cluster inP. aeruginosastrain ZK2870 and identify a second genetic locus, termedpsl, involved in the production of a mannose-rich matrix material. The 11 predicted protein products of thepslgenes are homologous to proteins involved in carbohydrate processing.P. aeruginosais thus able to produce two distinct carbohydrate-rich matrix materials. Either carbohydrate-rich matrix component appears to be sufficient for mature biofilm formation, and at least one of them is required for mature biofilm formation inP. aeruginosastrains PA14 and ZK2870.
Identification ofpsl, a Locus Encoding a Potential Exopolysaccharide That Is Essential forPseudomonas aeruginosaPAO1 Biofilm Formation
Authors: Jackson Kara D. , Starkey Melissa , Kremer Stefanie , Parsek Matthew R. , Wozniak Daniel J. 
Published: July 2004

ABSTRACTBacteria inhabiting biofilms usually produce one or more polysaccharides that provide a hydrated scaffolding to stabilize and reinforce the structure of the biofilm, mediate cell-cell and cell-surface interactions, and provide protection from biocides and antimicrobial agents. Historically, alginate has been considered the major exopolysaccharide of thePseudomonas aeruginosabiofilm matrix, with minimal regard to the different functions polysaccharides execute. Recent chemical and genetic studies have demonstrated that alginate is not involved in the initiation of biofilm formation inP. aeruginosastrains PAO1 and PA14. We hypothesized that there is at least one other polysaccharide gene cluster involved in biofilm development. Two separate clusters of genes with homology to exopolysaccharide biosynthetic functions were identified from the annotated PAO1 genome. Reverse genetics was employed to generate mutations in genes from these clusters. We discovered that one group of genes, designatedpsl, are important for biofilm initiation. A PAO1 strain with a disruption of the first two genes of thepslcluster (PA2231 and PA2232) was severely compromised in biofilm initiation, as confirmed by static microtiter and continuous culture flow cell and tubing biofilm assays. This impaired biofilm phenotype could be complemented with the wild-typepslsequences and was not due to defects in motility or lipopolysaccharide biosynthesis. These results implicate an as yet unknown exopolysaccharide as being required for the formation of the biofilm matrix. Understandingpsl-encoded exopolysaccharide expression and protection in biofilms will provide insight into the pathogenesis ofP. aeruginosain cystic fibrosis and other infections involving biofilms.
SadB Is Required for the Transition from Reversible to Irreversible Attachment during Biofilm Formation by
Pseudomonas aeruginosa
PA14
Authors: Caiazza Nicky C. , O'Toole George A. 
Published: July 2004

ABSTRACT

Current models of biofilm formation by
Pseudomonas aeruginosa
propose that (i) planktonic cells become surface associated in a monolayer, (ii) surface-associated cells form microcolonies by clonal growth and/or aggregation, (iii) microcolonies transition to a mature biofilm comprised of exopolysaccharide-encased macrocolonies, and (iv) cells exit the mature biofilm and reenter the planktonic state. Here we report a new class of
P. aeruginosa
biofilm mutant that defines the transition from reversible to irreversible attachment and is thus required for monolayer formation. The transposon insertion carried by the
sadB199
mutant was mapped to open reading frame PA5346 of
P. aeruginosa
PA14 and encodes a protein of unknown function. Complementation analysis and phage-mediated transduction demonstrated that the transposon insertion in PA5346 was the cause of the biofilm-defective phenotype. Examination of flow cell-grown biofilms showed that the
sadB199
mutant could initiate surface attachment but failed to form microcolonies despite being proficient in both twitching and swimming motility. Closer examination of early attachment revealed an increased number of the
sadB199
mutant cells arrested at reversible attachment, functionally defined as adherence via the cell pole. A positive correlation among biofilm formation, irreversible attachment, and SadB level was demonstrated, and furthermore, RpoN and FleR appear to negatively affect SadB levels. Fractionation studies showed that the SadB protein is localized to the cytoplasm, and with the use of GPS-linker scanning mutagenesis, the C-terminal portion of SadB was shown to be dispensable for function, whereas the two putative domains of unknown function and the linker region spanning these domains were required for function. We discuss the results presented here in the context of microbial development as it applies to biofilm formation.
Genes Regulated by TorR, the Trimethylamine Oxide Response Regulator of
Shewanella oneidensis
Authors: Bordi Christophe , Ansaldi Mireille , Gon Stéphanie , Jourlin-Castelli Cécile , Iobbi-Nivol Chantal , Méjean Vincent 
Published: July 2004

ABSTRACT

The
torECAD
operon encoding the trimethylamine oxide (TMAO) respiratory system of
Shewanella oneidensis
is positively controlled by the TorS/TorR two-component system when TMAO is available. Activation of the
tor
operon occurs upon binding of the phosphorylated response regulator TorR to a single operator site containing the direct repeat nucleotide sequence TTCATAN
4
TTCATA. Here we show that the replacement of any nucleotide of one TTCATA hexamer prevented TorR binding in vitro, meaning that TorR specifically interacts with this DNA target. Identical direct repeat sequences were found in the promoter regions of
torR
and of the new gene
torF
(
SO4694
), and they allowed TorR binding to both promoters. Real-time PCR experiments revealed that
torR
is negatively autoregulated, whereas
torF
is strongly induced by TorR in response to TMAO. Transcription start site location and footprinting analysis indicate that the operator site at
torR
overlaps the promoter −10 box, whereas the operator site at
torF
is centered at −74 bp from the start site, in agreement with the opposite role of TorR in the regulation of the two genes. Since
torF
and
torECAD
are positively coregulated by TorR, we propose that the TorF protein plays a role related to TMAO respiration.
Flexibility in the Receptor-Binding Domain of the Enzymatic Colicin E9 Is Required for Toxicity against
Escherichia coli
Cells
Authors: Penfold Christopher N. , Healy Bryan , Housden Nicholas G. , Boetzel Ruth , Vankemmelbeke Mireille , Moore Geoffrey R. , Kleanthous Colin , James Richard 
Published: July 2004

ABSTRACT

The events that occur after the binding of the enzymatic E colicins to
Escherichia coli
BtuB receptors that lead to translocation of the cytotoxic domain into the periplasmic space and, ultimately, cell killing are poorly understood. It has been suggested that unfolding of the coiled-coil BtuB receptor binding domain of the E colicins may be an essential step that leads to the loss of immunity protein from the colicin and immunity protein complex and then triggers the events of translocation. We introduced pairs of cysteine mutations into the receptor binding domain of colicin E9 (ColE9) that resulted in the formation of a disulfide bond located near the middle or the top of the R domain. After dithiothreitol reduction, the ColE9 protein with the mutations L359C and F412C (ColE9 L359C-F412C) and the ColE9 protein with the mutations Y324C and L447C (ColE9 Y324C-L447C) were slightly less active than equivalent concentrations of ColE9. On oxidation with diamide, no significant biological activity was seen with the ColE9 L359C-F412C and the ColE9 Y324C-L447C mutant proteins; however diamide had no effect on the activity of ColE9. The presence of a disulfide bond was confirmed in both of the oxidized, mutant proteins by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The loss of biological activity of the disulfide-containing mutant proteins was not due to an indirect effect on the properties of the translocation or DNase domains of the mutant colicins. The data are consistent with a requirement for the flexibility of the coiled-coil R domain after binding to BtuB.
The
Bacillus subtilis yqjI
Gene Encodes the NADP
+
-Dependent 6-P-Gluconate Dehydrogenase in the Pentose Phosphate Pathway
Authors: Zamboni Nicola , Fischer Eliane , Laudert Dietmar , Aymerich Stéphane , Hohmann Hans-Peter , Sauer Uwe 
Published: July 2004

ABSTRACT

Despite the importance of the oxidative pentose phosphate (PP) pathway as a major source of reducing power and metabolic intermediates for biosynthetic processes, almost no direct genetic or biochemical evidence is available for
Bacillus subtilis
. Using a combination of knockout mutations in known and putative genes of the oxidative PP pathway and
13
C-labeling experiments, we demonstrated that
yqjI
encodes the NADP
+
-dependent 6-P-gluconate dehydrogenase, as was hypothesized previously from sequence similarities. Moreover, YqjI was the predominant isoenzyme during glucose and gluconate catabolism, and its role in the oxidative PP pathway could not be played by either of two homologues, GntZ and YqeC. This conclusion is in contrast to the generally held view that GntZ is the relevant isoform; hence, we propose a new designation for
yqjI
,
gndA
, the monocistronic gene encoding the principal 6-P-gluconate dehydrogenase. Although we demonstrated the NAD
+
-dependent 6-P-gluconate dehydrogenase activity of GntZ,
gntZ
mutants exhibited no detectable phenotype on glucose, and GntZ did not contribute to PP pathway fluxes during growth on glucose. Since
gntZ
mutants grew normally on gluconate, the functional role of GntZ remains obscure, as does the role of the third homologue, YqeC. Knockout of the glucose-6-P dehydrogenase-encoding
zwf
gene was primarily compensated for by increased glycolytic fluxes, but about 5% of the catabolic flux was rerouted through the gluconate bypass with glucose dehydrogenase as the key enzyme.
Long-Term Anaerobic Survival of the Opportunistic Pathogen
Pseudomonas aeruginosa
via Pyruvate Fermentation
Authors: Eschbach Martin , Schreiber Kerstin , Trunk Katharina , Buer Jan , Jahn Dieter , Schobert Max 
Published: July 2004

ABSTRACT

Denitrification and arginine fermentation are central metabolic processes performed by the opportunistic pathogen
Pseudomonas aeruginosa
during biofilm formation and infection of lungs of patients with cystic fibrosis. Genome-wide searches for additional components of the anaerobic metabolism identified potential genes for pyruvate-metabolizing NADH-dependent lactate dehydrogenase (
ldhA
), phosphotransacetylase (
pta
), and acetate kinase (
ackA
). While pyruvate fermentation alone does not sustain significant anaerobic growth of
P. aeruginosa
, it provides the bacterium with the metabolic capacity for long-term survival of up to 18 days. Detected conversion of pyruvate to lactate and acetate is dependent on the presence of intact
ldhA
and
ackA-pta
loci, respectively. DNA microarray studies in combination with reporter gene fusion analysis and enzyme activity measurements demonstrated the
anr
- and
ihfA-
dependent anaerobic induction of the
ackA-pta
promoter. Potential Anr and integration host factor binding sites were localized. Pyruvate-dependent anaerobic long-term survival was found to be significantly reduced in
anr
and
ihfA
mutants. No obvious
ldhA
regulation by oxygen tension was observed. Pyruvate fermentation is pH dependent. Nitrate respiration abolished pyruvate fermentation, while arginine fermentation occurs independently of pyruvate utilization.
The CorA Mg
2+
Transporter Is a Homotetramer
Authors: Warren Mary Ann , Kucharski Lisa M. , Veenstra Alexander , Shi Liang , Grulich Paul F. , Maguire Michael E. 
Published: July 2004

ABSTRACT

CorA is a primary Mg
2+
transporter for
Bacteria
and
Archaea
. The C-terminal domain of ∼80 amino acids forms three transmembrane (TM) segments, which suggests that CorA is a homo-oligomer. A Cys residue was added to the cytoplasmic C terminus (C317) of
Salmonella enterica
serovar Typhimurium CorA with or without mutation of the single periplasmic Cys191 to Ser; each mutant retained function. Oxidation of the Cys191Ser Cys317 CorA gave a dimer. Oxidation of Cys317 CorA showed a dimer plus an additional band, apparently cross-linked via both Cys317 and C191. To determine oligomer order, intact cells or purified membranes were treated with formaldehyde or carbon disulfide. Higher-molecular-mass bands formed, consistent with the presence of a tetramer. Cross-linking of the
Bacillus subtilis
CorA expressed in
Salmonella
serovar Typhimurium similarly indicated a tetramer. CorA periplasmic soluble domains from both
Salmonella
serovar Typhimurium and the archaeon
Methanococcus jannaschii
were purified and shown to retain structure. Formaldehyde treatment showed formation of a tetramer. Finally, previous mutagenesis of the CorA membrane domain identified six intramembrane residues forming an apparent pore that interacts with Mg
2+
during transport. Each was mutated to Cys. In mutants carrying a single intramembrane Cys residue, spontaneous disulfide bond formation that was enhanced by oxidation with Cu(II)-1,10-phenanthroline was observed between monomers, indicating that these Mg
2+
-interacting residues within the membrane are very close to their cognate residue on another monomer. Thus, CorA appears to be a homotetramer with a TM segment of one monomer physically close to the same TM segment of another monomer.
The
Vibrio cholerae
FlgM Homologue Is an Anti-σ
28
Factor That Is Secreted through the Sheathed Polar Flagellum
Authors: Correa Nidia E. , Barker Jeffrey R. , Klose Karl E. 
Published: July 2004

ABSTRACT

Vibrio cholerae
has a single polar sheathed flagellum that propels the cells of this bacterium. Flagellar synthesis, motility, and chemotaxis have all been linked to virulence in this human pathogen.
V. cholerae
expresses flagellar genes in a hierarchy consisting of σ
54
- and σ
28
-dependent transcription. In other bacteria, σ
28
transcriptional activity is controlled by an anti-σ
28
factor, FlgM. We demonstrate that the
V. cholerae
FlgM homologue (i) physically interacts with σ
28
, (ii) has a repressive effect on some
V. cholerae
σ
28
-dependent flagellar promoters, and (iii) is secreted through the polar sheathed flagellum, consistent with anti-σ
28
activity. Interestingly, FlgM does not have a uniform repressive effect on all σ
28
-dependent promoters, as determined by measurement of σ
28
-dependent transcription in cells either lacking FlgM (Δ
flgM
) or incapable of secretion (Δ
fliF
). Further analysis of a Δ
fliF
strain revealed that this flagellar assembly block causes a decrease in class III (FlrC- and σ
54
-dependent) and class IV (σ
28
-dependent), but not class II (FlrA- and σ
54
-dependent), flagellar transcription.
V. cholerae flgM
and
fliA
(encodes σ
28
) mutants were only modestly affected in their ability to colonize the infant mouse intestine, a measure of virulence. Our results demonstrate that
V. cholerae
FlgM functions as an anti-σ
28
factor and that the sheathed flagellum is competent for secretion of nonstructural proteins.
Structure and Electrophysiological Properties of the YscC Secretin from the Type III Secretion System of
Yersinia enterocolitica
Authors: Burghout Peter , van Boxtel Ria , Van Gelder Patrick , Ringler Philippe , Müller Shirley A. , Tommassen Jan , Koster Margot 
Published: July 2004

ABSTRACT

YscC is the integral outer membrane component of the type III protein secretion machinery of
Yersinia enterocolitica
and belongs to the family of secretins. This group of proteins forms stable ring-like oligomers in the outer membrane, which are thought to function as transport channels for macromolecules. The YscC oligomer was purified after solubilization from the membrane with a nonionic detergent. Sodium dodecyl sulfate did not dissociate the oligomer, but it caused a change in electrophoretic mobility and an increase in protease susceptibility, indicating partial denaturation of the subunits within the oligomer. The mass of the homo-oligomer, as determined by scanning transmission electron microscopy, was approximately 1 MDa. Analysis of the angular power spectrum from averaged top views of negatively stained YscC oligomers revealed a 13-fold angular order, suggesting that the oligomer consists of 13 subunits. Reconstituted in planar lipid bilayers, the YscC oligomer displayed a constant voltage-independent conductance of approximately 3 nS, thus forming a stable pore. However, in vivo, the expression of YscC did not lead to an increased permeability of the outer membrane. Electron microscopy revealed that the YscC oligomer is composed of three domains, two stacked rings attached to a conical domain. This structure is consistent with the notion that the secretin forms the upper part of the basal body of the needle structure of the type III secreton.
Response ofBacillus subtilisto Nitric Oxide and the Nitrosating Agent Sodium Nitroprusside
Authors: Moore Charles M. , Nakano Michiko M. , Wang Tao , Ye Rick W. , Helmann John D. 
Published: July 2004

ABSTRACTWe examined the effects of nitric oxide (NO) and sodium nitroprusside (SNP) onBacillus subtilisphysiology and gene expression. In aerobically growing cultures, cell death was most pronounced when NO gas was added incrementally rather than as a single bolus, suggesting that the length of exposure was important in determining cell survival. DNA microarrays, Northern hybridizations, and RNA slot blot analyses were employed to characterize the global transcriptional response ofB. subtilisto NO and SNP. Under both aerobic and anaerobic conditions the gene most highly induced by NO washmp, a flavohemoglobin known to protect bacteria from NO stress. Anaerobically, NO also induced genes repressed by the Fe(II)-containing metalloregulators, Fur and PerR, consistent with the known ability of NO to nitrosylate the Fe(II) center in Fur. In support of this model, we demonstrate that NO fails to induce PerR-regulated genes under growth conditions that favor the formation of PerR:Mn(II) rather than PerR:Fe(II). Aerobically, NO gas inducedhmp, the σBgeneral stress regulon, and, to a lesser extent, the Fur and PerR regulons. Surprisingly, NO gas induced the σBregulon via the energy branch of the σBregulatory cascade while induction by SNP was mediated by the environmental stress branch. This emphasizes that NO and SNP elicit genetically distinct stress responses.
Global Gene Expression in
Staphylococcus aureus
Biofilms
Authors: Beenken Karen E. , Dunman Paul M. , McAleese Fionnuala , Macapagal Daphne , Murphy Ellen , Projan Steven J. , Blevins Jon S. , Smeltzer Mark S. 
Published: July 2004

ABSTRACT

We previously demonstrated that mutation of the staphylococcal accessory regulator (
sarA
) in a clinical isolate of
Staphylococcus aureus
(UAMS-1) results in an impaired capacity to form a biofilm in vitro (K. E. Beenken, J. S. Blevins, and M. S. Smeltzer, Infect. Immun. 71:4206-4211, 2003). In this report, we used a murine model of catheter-based biofilm formation to demonstrate that a UAMS-1
sarA
mutant also has a reduced capacity to form a biofilm in vivo. Surprisingly, mutation of the UAMS-1
ica
locus had little impact on biofilm formation in vitro or in vivo. In an effort to identify additional loci that might be relevant to biofilm formation and/or the adaptive response required for persistence of
S. aureus
within a biofilm, we isolated total cellular RNA from UAMS-1 harvested from a biofilm grown in a flow cell and compared the transcriptional profile of this RNA to RNA isolated from both exponential- and stationary-phase planktonic cultures. Comparisons were done using a custom-made Affymetrix GeneChip representing the genomic complement of six strains of
S. aureus
(COL, N315, Mu50, NCTC 8325, EMRSA-16 [strain 252], and MSSA-476). The results confirm that the sessile lifestyle associated with persistence within a biofilm is distinct by comparison to the lifestyles of both the exponential and postexponential phases of planktonic culture. Indeed, we identified 48 genes in which expression was induced at least twofold in biofilms over expression under both planktonic conditions. Similarly, we identified 84 genes in which expression was repressed by a factor of at least 2 compared to expression under both planktonic conditions. A primary theme that emerged from the analysis of these genes is that persistence within a biofilm requires an adaptive response that limits the deleterious effects of the reduced pH associated with anaerobic growth conditions.