bluuebunny/crossref_metadata_2025 huggingface dataset:
Specific Control of Endogenous cCF10 Pheromone by a Conserved Domain of the pCF10-Encoded Regulatory Protein PrgY inEnterococcus faecalis
Authors: Chandler Josephine R. , Flynn Aron R. , Bryan Edward M. , Dunny Gary M.
Published: July 2005

Conjugative transfer ofEnterococcus faecalisplasmid pCF10 is induced by the heptapeptide pheromone cCF10. cCF10 produced by plasmid-free recipient cells is detected by pCF10-containing donor cells, which respond by induction of plasmid-encoded transfer functions. The pCF10-encoded membrane protein PrgY is essential to prevent donor cells from responding to endogenously produced pheromone while maintaining the ability to respond to pheromone from an exogenous source; this function has not been identified in any nonenterococcal prokaryotic signaling system. PrgY specifically inhibited endogenous cCF10 and cPD1 (a pheromone that induces transfer of closely related plasmid pPD1) but not cAD1 (which is specific for less-related plasmid pAD1). Ectopic expression of PrgY in plasmid-free recipient cells reduced pheromone activity in culture supernatants and reduced the ability of these cells to acquire pCF10 by conjugation but did not have any effect on the interaction of these cells with exogenously supplied cCF10. The clonedprgYgene could complement a pCF10prgYnull mutation, and complementation was used to identify point mutations impairing PrgY function. Such mutations also abolished the inhibitory effect of PrgY expression in recipients on pheromone production and on acquisition of pCF10. Most randomly generated point mutations identified in the genetic screen mapped to a predicted extracellular domain in the N terminus of PrgY that is conserved in a newly identified family of related proteins from disparate species includingBorrelia burgdorferi,Archaeoglobus fulgidus,Arabidopsis thaliana, andHomo sapiens. The combined genetic and physiological data suggest that PrgY may sequester or inactivate cCF10 as it is released from the membrane.
Citrate Synthase Mutants of
Agrobacterium
Are Attenuated in Virulence and Display Reduced
vir
Gene Induction
Authors: Suksomtip Maneewan , Liu Pu , Anderson Tamara , Tungpradabkul Sumalee , Wood Derek W. , Nester Eugene W.
Published: July 2005

A citrate synthase (CS) deletion mutant of
Agrobacterium tumefaciens
C58 is highly attenuated in virulence. The identity of the mutant was initially determined from its amino acid sequence, which is 68% identical to
Escherichia coli
and 77% identical to
Brucella melitensis
. The mutant lost all CS enzymatic activity, and a cloned CS gene complemented a CS mutation in
Sinorhizobium
. The CS mutation resulted in a 10-fold reduction in
vir
gene expression, which likely accounts for the attenuated virulence. When a plasmid containing a constitutive
virG
[
virG
(Con)] locus was introduced into this mutant, the level of
vir
gene induction was restored to nearly wild-type level. Further, the
virG
(Con)-complemented CS mutant strain induced tumors that were similar in size and number to those induced by the parental strain. The CS mutation resulted in only a minor reduction in growth rate in a glucose-salts medium. Both the CS mutant and the
virG
(Con)-complemented CS strain displayed similar growth deficiencies in a glucose-salts medium, indicating that the reduced growth rate of the CS mutant could not be responsible for the attenuated virulence. A search of the genome of
A. tumefaciens
C58 revealed four proteins, encoded on different replicons, with conserved CS motifs. However, only the locus that when mutated resulted in an attenuated phenotype has CS activity. Mutations in the other three loci did not result in attenuated virulence and any loss of CS activity, and none were able to complement the CS mutation in
Sinorhizobium
. The function of these loci remains unknown.
Global Analysis of Cellular Factors and Responses Involved inPseudomonas aeruginosaResistance to Arsenite
Authors: Parvatiyar Kislay , Alsabbagh Eyad M. , Ochsner Urs A. , Stegemeyer Michelle A. , Smulian Alan G. , Hwang Sung Hei , Jackson Colin R. , McDermott Timothy R. , Hassett Daniel J.
Published: July 2005

The impact of arsenite [As(III)] on several levels of cellular metabolism and gene regulation was examined inPseudomonas aeruginosa. P. aeruginosaisogenic mutants devoid of antioxidant enzymes or defective in various metabolic pathways, DNA repair systems, metal storage proteins, global regulators, or quorum sensing circuitry were examined for their sensitivity to As(III). Mutants lacking the As(III) translocator (ArsB), superoxide dismutase (SOD), catabolite repression control protein (Crc), or glutathione reductase (Gor) were more sensitive to As(III) than wild-type bacteria. The MICs of As(III) under aerobic conditions were 0.2, 0.3, 0.8, and 1.9 mM forarsB,sodA sodB,crc, andgormutants, respectively, and were 1.5- to 13-fold less than the MIC for the wild-type strain. A two-dimensional gel/matrix-assisted laser desorption ionization-time of flight analysis of As(III)-treated wild-type bacteria showed significantly (>40-fold) increased levels of a heat shock protein (IbpA) and a putative allo-threonine aldolase (GlyI). Smaller increases (up to 3.1-fold) in expression were observed for acetyl-coenzyme A acetyltransferase (AtoB), a probable aldehyde dehydrogenase (KauB), ribosomal protein L25 (RplY), and the probable DNA-binding stress protein (PA0962). In contrast, decreased levels of a heme oxygenase (HemO/PigA) were found upon As(III) treatment. Isogenic mutants were successfully constructed for six of the eight genes encoding the aforementioned proteins. When treated with sublethal concentrations of As(III), each mutant revealed a marginal to significant lag period prior to resumption of apparent normal growth compared to that observed in the wild-type strain. Our results suggest that As(III) exposure results in an oxidative stress-like response inP. aeruginosa, although activities of classic oxidative stress enzymes are not increased. Instead, relief from As(III)-based oxidative stress is accomplished from the collective activities of ArsB, glutathione reductase, and the global regulator Crc. SOD appears to be involved, but its function may be in the protection of superoxide-sensitive sulfhydryl groups.
Identification of the Iron-Responsive Genes of
Neisseria gonorrhoeae
by Microarray Analysis in Defined Medium
Authors: Ducey Thomas F. , Carson Matthew B. , Orvis Joshua , Stintzi Alain P. , Dyer David W.
Published: July 2005

To ensure survival, most bacteria must acquire iron, a resource that is sequestered by mammalian hosts. Pathogenic bacteria have therefore evolved intricate systems to sense iron limitation and regulate gene expression appropriately. We used a pan-
Neisseria
microarray to examine genes regulated in
Neisseria gonorrhoeae
in response to iron availability in defined medium. Overall, 203 genes varied in expression, 109 up-regulated and 94 down-regulated by iron deprivation. In iron-replete medium, genes essential to rapid bacterial growth were preferentially expressed, while iron transport functions, and predominantly genes of unknown function, were expressed in low-iron medium. Of those TonB-dependent proteins encoded in the FA1090 genome with unknown ligand specificity, expression of three was not controlled by iron availability, suggesting that these receptors may not be high-affinity transporters for iron-containing ligands. Approximately 30% of the operons regulated by iron appeared to be directly under control of Fur. Our data suggest a regulatory cascade where Fur indirectly controls gene expression by affecting the transcription of three secondary regulators. Our data also suggest that a second MerR-like regulator may be directly responding to iron availability and controlling transcription independent of the Fur protein. Comparison of our data with those recently published for
Neisseria meningitidis
revealed that only a small portion of genes were found to be similarly regulated in these closely related pathogens, while a large number of genes derepressed during iron starvation were unique to each organism.
Quorum-Sensing-Negative (
lasR
) Mutants of
Pseudomonas aeruginosa
Avoid Cell Lysis and Death
Authors: Heurlier Karin , Dénervaud Valérie , Haenni Marisa , Guy Lionel , Krishnapillai Viji , Haas Dieter
Published: July 2005

In
Pseudomonas aeruginosa
,
N
-acylhomoserine lactone signals regulate the expression of several hundreds of genes, via the transcriptional regulator LasR and, in part, also via the subordinate regulator RhlR. This regulatory network termed quorum sensing contributes to the virulence of
P. aeruginosa
as a pathogen. The fact that two supposed PAO1 wild-type strains from strain collections were found to be defective for LasR function because of independent point mutations in the
lasR
gene led to the hypothesis that loss of quorum sensing might confer a selective advantage on
P. aeruginosa
under certain environmental conditions. A convenient plate assay for LasR function was devised, based on the observation that
lasR
mutants did not grow on adenosine as the sole carbon source because a key degradative enzyme, nucleoside hydrolase (Nuh), is positively controlled by LasR. The wild-type PAO1 and
lasR
mutants showed similar growth rates when incubated in nutrient yeast broth at pH 6.8 and 37°C with good aeration. However, after termination of growth during 30 to 54 h of incubation, when the pH rose to ≥ 9, the
lasR
mutants were significantly more resistant to cell lysis and death than was the wild type. As a consequence, the
lasR
mutant-to-wild-type ratio increased about 10-fold in mixed cultures incubated for 54 h. In a PAO1 culture, five consecutive cycles of 48 h of incubation sufficed to enrich for about 10% of spontaneous mutants with a Nuh
−
phenotype, and five of these mutants, which were functionally complemented by
lasR

+

, had mutations in
lasR
. The observation that, in buffered nutrient yeast broth, the wild type and
lasR
mutants exhibited similar low tendencies to undergo cell lysis and death suggests that alkaline stress may be a critical factor providing a selective survival advantage to
lasR
mutants.
Molecular Cloning and Transcriptional and Expression Analysis of
engO
, Encoding a New Noncellulosomal Family 9 Enzyme, from
Clostridium cellulovorans
Authors: Han Sung Ok , Yukawa Hideaki , Inui Masayuki , Doi Roy H.
Published: July 2005

Clostridium cellulovorans
produces a major noncellulosomal family 9 endoglucanase EngO. A genomic DNA fragment (40 kb) containing
engO
and neighboring genes was cloned. The nucleotide sequence contained reading frames for endoglucanase EngO, a putative response regulator, and a putative sensor histidine kinase protein. The
engO
gene consists of 2,172 bp and encodes a protein of 724 amino acids with a molecular weight of 79,474. Northern hybridizations revealed that the
engO
gene is transcribed as a monocistronic 2.6-kb mRNA. 5′ RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) PCR analysis indicated that the single transcriptional start site of
engO
was located 264 bp upstream from the first nucleotide of the translation initiation codon. Alignment of the
engO
promoter region provided evidence for highly conserved sequences that exhibited strong similarity to the σ
A
consensus promoter sequences of gram-positive bacteria. EngO contains a typical N-terminal signal peptide of 28 amino acid residues, followed by a 149-amino-acid sequence which is homologous to the family 4-9 carbohydrate-binding domain. Downstream of this domain was an immunoglobulin-like domain of 89 amino acids. The C terminus contains a family 9 catalytic domain of glycosyl hydrolase. Mass spectrometry analysis of EngO was in agreement with that deduced from the nucleotide sequence. Expression of
engO
mRNA increased from early to middle exponential phase and decreased during the early stationary phase. EngO was highly active toward carboxymethyl cellulose but showed no activity towards xylan. It was optimally active at 40 to 50°C and pH 5 to 6. The analysis of the products from the cellulose hydrolysis through thin-layer chromatography indicated its endoglucanase activity.
Hierarchical Control of Anaerobic Gene Expression in
Escherichia coli
K-12: the Nitrate-Responsive NarX-NarL Regulatory System Represses Synthesis of the Fumarate-Responsive DcuS-DcuR Regulatory System
Authors: Goh Ee-Been , Bledsoe Peggy J. , Chen Li-Ling , Gyaneshwar Prasad , Stewart Valley , Igo Michele M.
Published: July 2005

Hierarchical control ensures that facultative bacteria preferentially use the available respiratory electron acceptor with the most positive standard redox potential. Thus, nitrate is used before other electron acceptors such as fumarate for anaerobic respiration. Nitrate regulation is mediated by the NarX-NarL two-component system, which activates the transcription of operons encoding nitrate respiration enzymes and represses the transcription of operons for other anaerobic respiratory enzymes, including enzymes involved in fumarate respiration. These are fumarate reductase (encoded by the
frdABCD
operon), fumarase B, which generates fumarate from malate, and the DcuB permease for fumarate, malate, and aspartate. The transcription of the corresponding structural genes is activated by the DcuS-DcuR two-component system in response to fumarate or its dicarboxylate precursors. We report results from preliminary transcription microarray experiments that revealed two previously unknown members of the NarL regulon: the
aspA
gene encoding aspartate-ammonia lyase, which generates fumarate; and the
dcuSR
operon encoding the dicarboxylate-responsive regulatory system. We measured beta-galactosidase expression from monocopy
aspA-lacZ
,
frdA-lacZ
, and
dcuS-lacZ
operon fusions in response to added nitrate and fumarate and with respect to the
dcuR
and
narL
genotypes. Nitrate, acting through the NarX-NarL regulatory system, repressed the transcription of all three operons. Only
frdA-lacZ
expression, however, was responsive to added fumarate or a
dcuR

+

genotype. Phospho-NarL protein protected operator sites in the
aspA
and
dcuS
promoter regions from DNase I cleavage in vitro. The overall results are consistent with the hypothesis that nitrate represses
frdA
operon transcription not only directly, by repressing
frdA
promoter activity, but also indirectly, by repressing
dcuS
promoter activity.
Rapid Detection of Colicin E9-Induced DNA Damage Using
Escherichia coli
Cells Carrying SOS Promoter-
lux
Fusions
Authors: Vankemmelbeke Mireille , Healy Bryan , Moore Geoffrey R. , Kleanthous Colin , Penfold Christopher N. , James Richard
Published: July 2005

ColE9 is a plasmid-encoded protein antibiotic produced by
Escherichia coli
and closely related species that kills
E. coli
cells expressing the BtuB receptor. The 15-kDa cytotoxic DNase domain of colicin E9 preferentially nicks double-stranded DNA at thymine bases and shares a common active-site structural motif with a variety of other nucleases, including the H-N-H homing endonucleases and the apoptotic CAD proteins of eukaryotes. Studies of the mechanism by which the DNase domain of ColE9 reaches the cytoplasm of
E. coli
cells are limited by the lack of a rapid, sensitive assay for the DNA damage that results. Here, we report the development of an SOS promoter-
lux
fusion reporter system for monitoring DNA damage in colicin-treated cells and illustrate the value of this reporter system in experiments that probe the mechanism and time required for the DNase domain of colicin E9 to reach the cytoplasm.
A Cystic Fibrosis Epidemic Strain of
Pseudomonas aeruginosa
Displays Enhanced Virulence and Antimicrobial Resistance
Authors: Salunkhe Prabhakar , Smart Catherine H. M. , Morgan J. Alun W. , Panagea Stavroula , Walshaw Martin J. , Hart C. Anthony , Geffers Robert , Tümmler Burkhard , Winstanley Craig
Published: July 2005

The Liverpool epidemic strain (LES) of
Pseudomonas aeruginosa
is a transmissible aggressive pathogen of cystic fibrosis (CF) patients. We compared transcriptome profiles of two LES isolates with each other and with a laboratory and genetic reference strain (PAO1) after growth to late exponential phase and following exposure to oxidative stress. Both LES isolates exhibited enhanced antimicrobial resistances linked to specific mutations in efflux pump genes. Although transcription of AmpC β-lactamase was up-regulated in both, one LES isolate contained a specific mutation rendering the
ampC
gene untranslatable. The virulence-related quorum-sensing (QS) regulon of LES431, an isolate that caused pneumonia in the non-CF parent of a CF patient, was considerably up-regulated in comparison to either isolate LES400, associated with a chronic CF infection, or strain PAO1. Premature activation of QS genes was detected in isolates from both non-CF parents and the CF patient in a previously reported infection episode. LES isolates lacking the up-regulated QS phenotype contained different frameshift mutations in
lasR
. When fed to
Drosophila melanogaster
, isolate LES431 killed the fruit flies more readily than either isolate LES400 or strain PAO1, indicating that virulence varies intraclonally. The LES may represent a clone with enhanced virulence and antimicrobial resistance characteristics that can vary or are lost due to mutations during long-term colonization but have contributed to the successful spread of the lineage throughout the CF population of the United Kingdom.
An Atypical KdpD Homologue from the CyanobacteriumAnabaenasp. Strain L-31: Cloning, In Vivo Expression, and Interaction withEscherichia coliKdpD-CTD
Authors: Ballal Anand , Bramkamp Marc , Rajaram Hema , Zimmann Petra , Apte Shree Kumar , Altendorf Karlheinz
Published: July 2005

ThekdpFABCoperon ofEscherichia coli, coding for the high-affinity K+transport system KdpFABC, is transcriptionally regulated by the products of the adjacently locatedkdpDEgenes. The KdpD protein is a membrane-bound sensor kinase consisting of a large N-terminal domain and a C-terminal transmitter domain interconnected by four transmembrane segments (the transmembrane segments together with the C-terminal transmitter domain of KdpD are referred to as CTD), while KdpE is a cytosolic response regulator. We have cloned and sequenced thekdpoperon from a nitrogen-fixing, filamentous cyanobacterium,Anabaenasp. strain L-31 (GenBank accession. numberAF213466). ThekdpABCgenes are similar in size to those ofE. coli, but thekdpDgene is short (coding only for 365 amino acids), showing homology only to the N-terminal domain ofE. coliKdpD. AkdpE-like gene is absent in the vicinity of this operon.AnabaenaKdpD with six C-terminal histidines was overproduced inE. coliand purified by Ni2+-nitrilotriacetic acid affinity chromatography. With antisera raised against the purifiedAnabaenaKdpD, the protein was detected inAnabaenasp. strain L-31 membranes. The membrane-associated or soluble form of theAnabaenaKdpD(6His) could be photoaffinity labeled with the ATP analog 8-azido-ATP, indicating the presence of an ATP binding site. The coproduction ofAnabaenaKdpD withE. coliKdpD-CTD decreasedE. coli kdpFABCexpression in response to K+limitation in vivo relative to the wild-type KdpD-CTD protein. In vitro experiments revealed that the kinase activity of theE. coliKdpD-CTD was unaffected, but its phosphatase activity increased in the presence ofAnabaenaKdpD(6His). To our knowledge this is the first report where a heterologous N-terminal domain (AnabaenaKdpD) is shown to affect intransKdpD-CTD (E. coli) activity, which is just opposite to that observed for the KdpD-N-terminal domain ofE. coli.
Genome-Wide Detection and Analysis of Cell Wall-Bound Proteins with LPxTG-Like Sorting Motifs
Authors: Boekhorst Jos , de Been Mark W. H. J. , Kleerebezem Michiel , Siezen Roland J.
Published: July 2005

Surface proteins of gram-positive bacteria often play a role in adherence of the bacteria to host tissue and are frequently required for virulence. A specific subgroup of extracellular proteins contains the cell wall-sorting motif LPxTG, which is the target for cleavage and covalent coupling to the peptidoglycan by enzymes called sortases. A comprehensive set of putative sortase substrates was identified by in silico analysis of 199 completely sequenced prokaryote genomes. A combination of detection methods was used, including secondary structure prediction, pattern recognition, sequence homology, and genome context information. With the hframe algorithm, putative substrates were identified that could not be detected by other methods due to errors in open reading frame calling, frameshifts, or sequencing errors. In total, 732 putative sortase substrates encoded in 49 prokaryote genomes were identified. We found striking species-specific variation for the LPxTG motif. A hidden Markov model (HMM) based on putative sortase substrates was created, which was subsequently used for the automatic detection of sortase substrates in recently completed genomes. A database was constructed, LPxTG-DB (
http://bamics3.cmbi.kun.nl/sortase_substrates
), containing for each genome a list of putative sortase substrates, sequence information of these substrates, the organism-specific HMMs based on the consensus sequence of the sortase recognition motif, and a graphic representation of this consensus.
Gene Transfer and Genome Plasticity inThermotoga maritima, a Model Hyperthermophilic Species
Authors: Mongodin Emmanuel F. , Hance Ioana R. , DeBoy Robert T. , Gill Steven R. , Daugherty Sean , Huber Robert , Fraser Claire M. , Stetter Karl , Nelson Karen E.
Published: July 2005

The genome sequence of the hyperthermophilic bacteriumThermotoga maritimaMSB8 presents evidence for lateral gene transfer events between bacterial and archaeal species. To estimate the extent of genomic diversity across the orderThermotogales, a comparative genomic hybridization study was initiated to compare nineThermotogastrains to the sequencedT. maritimaMSB8. Many differences could be associated with substrate utilization patterns, which are most likely a reflection of the environmental niche that these individual species occupy. A detailed analysis of some of the predicted variable regions demonstrates many examples of the deletion/insertion of complete cassettes of genes and of gene rearrangements and insertions of DNA within genes, with the C or N terminus being retained. Although the mechanism for gene transfer in this lineage remains to be elucidated, this analysis suggests possible associations with repetitive elements and highlights the possible benefits of rampant genetic exchange to these species.
Phenotypic and Transcriptional Characterization of the Meningococcal PhoPQ System, a Magnesium-Sensing Two-Component Regulatory System That Controls Genes Involved in Remodeling the Meningococcal Cell Surface
Authors: Newcombe J. , Jeynes J. C. , Mendoza E. , Hinds J. , Marsden G. L. , Stabler R. A. , Marti M. , McFadden J. J.
Published: July 2005

We previously identified and characterized a two-component regulatory system in the meningococcus with homology to the
phoP-phoQ
system in salmonella and showed that allele replacement of the NMB0595 regulator gene led to loss of virulence, sensitivity to antimicrobial peptides, perturbed protein expression, and magnesium-sensitive growth. On the basis of these findings we proposed that the system should be designated the meningococcal PhoPQ system. Here we further characterized the NMB0595 mutant and demonstrated that it had increased membrane permeability and was unable to form colonies on solid media with low magnesium concentrations, features that are consistent with disruption of PhoPQ-mediated modifications to the lipooligosaccharide structure. We examined the transcriptional profiles of wild-type and NMB0595 mutant strains and found that magnesium-regulated changes in gene expression are completely abrogated in the mutant, indicating that, similar to the salmonella PhoPQ system, the meningococcal PhoPQ system is regulated by magnesium. Transcriptional profiling of the mutant indicated that, also similar to the salmonella PhoPQ system, the meningococcal system is involved in control of virulence and remodeling of the bacterial cell surface in response to the host environment. The results are consistent with the hypothesis that the PhoP homologue plays a role in the meningococcus similar to the role played by PhoP in salmonella. Elucidating the role that the PhoPQ system and PhoPQ-regulated genes play in the response of the meningococcus to the host environment may provide new insights into the pathogenic process.
The Genome ofSulfolobus acidocaldarius, a Model Organism of theCrenarchaeota
Authors: Chen Lanming , Brügger Kim , Skovgaard Marie , Redder Peter , She Qunxin , Torarinsson Elfar , Greve Bo , Awayez Mariana , Zibat Arne , Klenk Hans-Peter , Garrett Roger A.
Published: July 2005

Sulfolobus acidocaldariusis an aerobic thermoacidophilic crenarchaeon which grows optimally at 80°C and pH 2 in terrestrial solfataric springs. Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted protein-encoding genes. Many of the smaller genes were identified for the first time on the basis of comparison of threeSulfolobusgenome sequences. Of the protein-coding genes, 305 are exclusive toS. acidocaldariusand 866 are specific to theSulfolobusgenus. Moreover, 82 genes for untranslated RNAs were identified and annotated. Owing to the probable absence of active autonomous and nonautonomous mobile elements, the genome stability and organization ofS. acidocaldariusdiffer radically from those ofSulfolobus solfataricusandSulfolobus tokodaii. TheS. acidocaldariusgenome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange inS. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of otherSulfolobusspecies. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly identified protein-coding genes forSulfolobus, are incorporated into a publicSulfolobusdatabase which can be accessed athttp://dac.molbio.ku.dk/dbs/Sulfolobus.
Localization of Translocation Complex Components in
Bacillus subtilis:
Enrichment of the Signal Recognition Particle Receptor at Early Sporulation Septa
Authors: Rubio Aileen , Jiang Xin , Pogliano Kit
Published: July 2005

We here demonstrate that in
Bacillus subtilis
, the signal recognition particle receptor, FtsY, transiently localizes to early sporulation septa, whereas three SecYEG translocase-associated membrane proteins (SecDF, SpoIIIJ, and YqjG) are uniformly distributed. These results suggest FtsY delivers secreted proteins to SecYEG at the septum, consistent with initial septal localization of forespore membrane proteins.
Characterization of the Multiple Transferable Resistance Repressor, MtrR, fromNeisseria gonorrhoeae
Authors: Hoffmann Katherine M. , Williams Daniel , Shafer William M. , Brennan Richard G.
Published: July 2005

MtrR represses expression of theNeisseria gonorrhoeae mtrCDEmultidrug efflux transporter genes. MtrR displays salt-dependent DNA binding, a stoichiometry of two dimers per DNA site, and, for a protein that was expected to be essentially all helical, a high percentage of random coil and possibly β-sheet structure.
The F
1
F
o
-ATP Synthase of
Mycobacterium smegmatis
Is Essential for Growth
Authors: Tran Sieu L. , Cook Gregory M.
Published: July 2005

The F
1
F
o
-ATP synthase plays an important role in a number of vital cellular processes in plants, animals, and microorganisms. In this study, we constructed a Δ
atpD
mutant of
Mycobacterium smegmatis
and demonstrated that
atpD
encoding the β subunit of the F
1
F
o
-ATP synthase is an essential gene in
M. smegmatis
during growth on nonfermentable and fermentable carbon sources.
Adenylyl Cyclase Activity of Cya1 from the Cyanobacterium
Synechocystis
sp. Strain PCC 6803 Is Inhibited by Bicarbonate
Authors: Masuda Shinji , Ono Taka-aki
Published: July 2005

Bicarbonate stimulates the activities of several class III adenylyl cyclases studied to date. However, we show here that bicarbonate decreased
V
max
and substrate affinity in Cya1, a major adenylyl cyclase in the cyanobacterium
Synechocystis
sp. strain PCC 6803. This indicates that manifestation of the bicarbonate responsiveness is specifically modulated in Cya1.
Photoresponsive Flagellum-Independent Motility of the Purple Phototrophic Bacterium
Rhodobacter capsulatus
Authors: Shelswell Kristopher J. , Taylor Terumi A. , Beatty J. Thomas
Published: July 2005

We report the discovery of photoresponsive, flagellum-independent motility of the α-proteobacterium
Rhodobacter capsulatus
, a nonsulfur purple phototrophic bacterium. This motility takes place in the 1.5% agar-glass interface of petri plates but not in soft agar, and cells move toward a light source. The appearances of motility assay plates inoculated with wild-type or flagellum-deficient mutants indicate differential contributions from flagellar and flagellum-independent mechanisms. Electron microscopy confirmed the absence of flagella in flagellar mutants and revealed the presence of pilus-like structures at one pole of wild-type and mutant cells. We suggest that
R. capsulatus
utilizes a flagellum-independent, photoresponsive mechanism that resembles twitching motility to move in a line away from the point of inoculation toward a light source.
Mutator Effects in
Escherichia coli
Caused by the Expression of Specific Foreign Genes
Authors: Gabrovsky Vanessa , Yamamoto Mitsuko Lynn , Miller Jeffrey H.
Published: July 2005

Certain genes from
Lactococcus lactis
and
Pseudomonas aeruginosa
, including the
nfxB
gene, generate a mutator phenotype in
Escherichia coli
. The results of this study, together with those of a previous study, support conservation of regulatory sequences in
E. coli
and
P. aeruginosa
and suggest that some efflux pumps prevent mutagenicity by exporting mutagenic products of metabolism.
Chemotactic Responses to Metals and Anaerobic Electron Acceptors in
Shewanella oneidensis
MR-1
Authors: Bencharit Sira , Ward Mandy J.
Published: July 2005

Although a previous study indicated that the dissimilatory metal-reducing bacterium
Shewanella oneidensis
MR-1 lacks chemotactic responses to metals that can be used as anaerobic electron acceptors, new results show that this bacterium responds to both Mn(III) and Fe(III). Cells were also shown to respond to another unusual electron acceptor, the humic acid analog anthraquinone-2,6-disulfonate. These results indicate that
S. oneidensis
is capable of moving towards a number of unusual anaerobic electron acceptors, including some that would normally be insoluble in the environment. Additionally,
S. oneidensis
was shown to migrate in gradients of several divalent cations under anaerobic conditions. Although responses to the reduced forms of redox-active metals, such as Mn(II) and Fe(II), might indicate that
S. oneidensis
uses gradients of these metals to locate the insoluble electron acceptors Mn(III/IV) and Fe(III) for dissimilatory purposes, responses to non-redox-active metals, such as Zn(II), suggest that movement towards divalent cations might serve other, potentially assimilatory, purposes.
Effect of
sdiA
on Biosensors of
N
-Acylhomoserine Lactones
Authors: Lindsay Amber , Ahmer Brian M. M.
Published: July 2005

Many gram-negative bacteria synthesize
N
-acylhomoserine lactones (AHLs) and then use transcription factors of the LuxR family to sense and respond to AHL accumulation in the environment; this phenomenon is termed quorum sensing. Bacteria produce a variety of AHLs, and numerous bacterial reporter strains, or biosensors, that can detect subsets of these molecules have been constructed. Many of these are based on
Escherichia coli
because this species does not produce AHLs. However, both
Escherichia
and
Salmonella
spp. contain a LuxR homolog named SdiA that can detect exogenous AHL synthesized by other microbial species. In this study we have determined that
sdiA
of
E. coli
and
Salmonella
spp. can activate an RhlR-based biosensor plasmid in response to AHLs other than what the biosensor was designed to detect. SdiA does not activate LuxR-, LasR-, or AhyR-based biosensor plasmids, although the presence of
sdiA
in
E. coli
does interfere with the function of the AhyR-based biosensor. Because
sdiA
interferes with the function of two of the four reporters, we have constructed a set of
E. coli
biosensor strains that lack
sdiA
. The set includes control reporters that allow the
luxR
dependence of responses to be determined.
Epitaxial Silicon Growth by Load-Lock Low Pressure Chemical Vapor Deposition System for Elevated Source/Drain Formation
Authors: Nakano Masayuki , Kotaki Hiroshi , Ohta Kenji , Shingubara Shoso
Published: July 2005

A silicon epitaxial layer on the active region of a Si substrate was selectively grown under a low temperature condition of 620°C with a low pressure chemical vapor deposition (LPCVD) employing SiH4 as a precursor, without high-temperature H2 annealing and ultra high vacuum chemical vapor deposition (UHV-CVD). This method was achieved by the use of a N2-purged wafer cassette and a load-lock chamber that was directly connected to the CVD chamber. A cross-sectional transmission electron microscopy (TEM) micrograph of the interface between the CVD-deposited film and the Si substrate revealed that the Si film was grown homoepitaxially, however nanometer-scaled silicon oxide islands were sparsely formed at the interface. Epitaxial film growth seemed to be achieved by lateral grain growth over oxide islands during film deposition. Polycrystalline Si was grown on the silicon oxide under the same deposition condition, and a Si epitaxial growth layer was formed on the active region selectively by wet chemical etching using HNO3, CH3COOH and HF-based solution. Since this system has higher throughput than conventional UHV-CVD or MBE systems, it is expected to become important for the development of future ULSI devices with a sub-50 nm-scale metal–oxide–semiconductor field effect transistor (MOSFET).
Temperature Coefficients of Refractive Indices of TiO2–SiO2 Films
Authors: Hirota Hidenobu , Itoh Mikitaka , Oguma Manabu , Hibino Yoshinori
Published: July 2005

We investigated the temperature coefficients of the refractive indices of TiO2–SiO2 films with different TiO2 concentrations at varying annealing temperature. We found that the temperature coefficients change from positive to negative in such films with a TiO2 concentration of more than 50 mol% in such a high-temperature annealing. We obtained a negative temperature coefficient of -4.7×10-5 1/°C for film with a TiO2 concentration of 74 mol%.
Three-Dimensional Atomic Image around Mn Atoms in Diluted Magnetic Semiconductor Zn0.4Mn0.6Te Obtained by X-Ray Fluorescence Holography
Authors: Hosokawa Shinya , Happo Naohisa , Hayashi Koichi , Takahashi Yukio , Ozaki Tōru , Horii Kenju , Matsubara Eiichiro
Published: July 2005

X-ray fluorescence holography (XFH) was applied at the beamline BL37XU of SPring-8 to visualize the three-dimensional local structure around the Mn atoms in a diluted magnetic semiconductor Zn0.4Mn0.6Te. The sample was irradiated by X-rays of certain energies beyond the Mn K absorption edge in order to obtain the Mn Kα fluorescence hologram. A three-dimensional atomic image around the Mn central atoms was derived from the hologram using Barton's algorithm. The nearest- and third-nearest-neighbor Te atoms were clearly visualized. However, the second-nearest-neighbor Zn or Mn atoms are barely visible in this image due to the small scattering efficiencies of these atoms.
The Leakage Current Conduction Mechanisms of Cu/Porous Silica Damascene Schemes with Nano-cluster TaSix Barrier
Authors: Chen Chung-Hsien , Chang Chin-Piao , Huang Fon-Shan
Published: July 2005

Leakage current conduction mechanisms of Cu/porous silica damascene structures with TaSi
x
(20 nm) barrier were investigated. Polycrystalline TaSi0.54 and nano-cluster TaSi0.42 barriers were prepared by dc sputtering with various power and pressure. The newly developed silica based slurry was employed for the metal-CMP of TaSi
x
films. The incorporation of traditional NH4OH solution and megasonic were applied to perform post-CMP cleaning. Auger mapping revealed clearly straight Cu and Ta lines in these TaSi
x
samples. The line-to-line leakage current density (J
L) was plotted versus the electric field (E) at various temperatures. The Ln(J
L)–(E)1/2 plots showed that Ln(J
L) is linearly dependent on (E)1/2, corresponding to Schottky emission mechanism. The slope of straight lines were determined from the data points of the Ln(J
L/T
2)–(1000/T) plots. It revealed the magnitude of barrier height. The maximum height of the potential barrier of nano-cluster TaSi
x
/porous silica is about 0.12–0.30 eV. The bias-temperature-stress induced leakage current was measured for reliability study.
Deposition of SiO2 by Plasma Enhanced Chemical Vapor Deposition as the Diffusion Barrier to Polymer Substrates
Authors: Jeong Chang Hyun , Lee June Hee , Lim Jong Tae , Cho Nam Gil , Moon Cheol Hee , Yeom Geun Young
Published: July 2005

SiO2 thin films were deposited at the temperatures <150°C by plasma enhanced chemical vapor deposition (PECVD) using a tetraethylorthosilicate (TEOS)/N2/O2 gas mixture, and the physical and chemical characteristics as well as the characteristics as a transparent diffusion barrier to H2O were investigated. Using a gas combination of TEOS(40 sccm)/O2(500 sccm)/N2(100 sccm) at source power of 500 W and dc bias voltage of -350 V, SiO2 with a stoichometric composition of SiO2 and a smooth surface similar to the substrate could be deposited. When a multilayer diffusion barrier composed of parylene(800 nm)/SiO2(100 nm)/parylene(800 nm)/SiO2(100 nm)/parylene(800 nm) was formed on a polyethersulfone (PES) substrate, the water vapor transmission rate (WVTR) of the substrate was decreased from 54.1 to 0.3 gm/(m2·day).
Plasma Emission Spectrochemical Analysis of the Surface State of Particles in a Suspension System
Authors: Kobayashi Kunpei , Sato Akira , Homma Tetsuya , Nagatomo Takao
Published: July 2005

A new analysis method for the surface state of particles was studied. The state of adhesion of SiO2 particles onto Y2O2S;Eu particles, obtained under different adhesion conditions, was examined by plasma emission spectrochemical analysis and by evaluation of the hydrophilic property of the powders. It was found out that this evaluation method was quite effective for understanding the relationship between the quality of coated film and the surface state of particles in a suspension and for controlling the coating process for forming pixels of display devices such as cathode ray tubes (CRTs).
Metal–Oxide–Semiconductor-Diode Characteristics with SiO2 Films Formed by Oxidation and Sputtering Using Electron-Cyclotron-Resonance-Plasma Stream
Authors: Saito Kunio , Jin Yoshito , Ono Toshiro , Shimada Masaru
Published: July 2005

The characteristics of oxidation using an electron-cyclotron-resonance (ECR)-plasma stream and metal–oxide–semiconductor (MOS) diodes were studied. Single-layer SiO2 films and stacked SiO2/SiO2 films were formed by oxidation and sputtering. The ECR-plasma stream was extracted using a divergent magnetic field and had ion energies of 10–30 eV. The oxidation of single-crystal Si substrates by the ECR-plasma stream provided a large SiO2 growth rate at the initial growth stage (>6 nm/min) with a very small activation energy of 0.02 eV. SiO2 film was sputter-deposited in the metal mode of reactive ECR sputtering on the SiO2 film previously formed by oxidation. The MOS diodes with the single-layer and stacked SiO2 films had high-quality SiO2/Si interfaces with interface-trap densities of 2×1010–3×1010 cm-2 eV-1, which were obtained by postdeposition annealing at 400°C in hydrogen-gas atmosphere. The SiO2 films formed by oxidation and the stacked SiO2 films provided breakdown fields greater than 11 MV/cm. The dependence of leakage current on measuring temperature was not observed for the stacked SiO2 films, indicating that the dominant conduction was Fowler–Nordheim tunneling.
In situ Observations of Orientational Ordering Process of 4'-n-pentyl-4-cyanobiphenyl Ultra-Thin Film Using Polarized Absorption Measurements
Authors: Taguchi Dai , Manaka Takaaki , Iwamoto Mitsumasa
Published: July 2005

Polarized optical absorption measurements were employed to study the orientational ordering process of 4'-n-pentyl-4-cyanobiphenyl (5CB) molecules deposited by the evaporation method. 5CB molecules were evaporated onto a silica substrate with and without ultra-thin polyimide films in a laboratory ambient atmosphere. The optical absorption of the films was measured during the deposition using linearly polarized UV light. The orientational order parameter S
2 was determined, even for regions of less than one monolayer thickness. The results clearly show that the orientational order is dependent on the substrate surface.
Surface Characteristics of Indium-Tin Oxide Cleaned by Remote Plasma
Authors: Kim Seokhoon , Seo Hyungtak , Kim Yangdo , Kim Kibeom , Tak Yoonheung , Jeon Hyeongtag
Published: July 2005

We investigated the remote oxygen and hydrogen plasma cleaning of indium-tin oxide and its surface electronic properties. Samples cleaned by hydrogen plasma after oxygen plasma cleaning showed the complete absence of surface contaminants while samples cleaned by only hydrogen or oxygen plasma showed some residual contaminants. Work function is mainly affected by oxygen plasma treatments while sheet resistance is more closely related to the removal of surface carbon contaminants. This study revealed that surface dipoles due to the O- ions are believed to have a more significant contribution to the change in work function than the reduction of Sn4+.
Simulation of Strain-Induced Microwrinkle Pattern Dynamics with Memory Effect
Authors: Ohzono Takuya , Shimomura Masatsugu
Published: July 2005

We computationally investigate the compression-induced reversible stripe rearrangement process, which is experimentally observed for the spontaneously formed pattern of microwrinkles on a Pt-sputtered elastomer surface. We propose a rough model for the wrinkles in a small bending regime considering the pattern memory of the neutral state with the strength parameter s, which should be attributable to the degree of material flow during initial pattern formation. The original pattern recovers after a compressive perturbation within finite time periods above the specific value of s. The simulated stripe rearrangement process shows qualitative agreement with the experimental results. In particular, the hysteretic behavior is reproduced and discussed in relation to s.
Effect of Precursor-Pulse on Properties of Al-Doped ZnO Films Grown by Atomic Layer Deposition
Authors: Kwon Sang Jik
Published: July 2005

Al-doped ZnO (ZnO:Al) films were grown by repeated sequential precursor reaction cycles (diethylzinc, Zn(C2H5)2; Ar purge; H2O; Ar purge; trimethylaluminum, Al(CH3)3) with a given pulse ratio of trimethylaluminum (TMA) to diethylzinc (DEZ). As the cycle ratio of TMA to DEZ (TMA/DEZ) increased, the resistivity of the films decreased and the roughness increased. For a TMA/DEZ pulse ratio of 1 to 10, the film had a resistivity of 9.7×10-4 Ω·cm and a roughness of 2.25 nm (rms), while for only DEZ injection, the film had a resistivity of 3.5×10-3 Ω·cm and a roughness of 1.07 nm (rms). The transmittance of the films was in excess of 80% for all samples with individually better performances corresponding to their respective wavelength ranges. For a successful atomic layer-controlled reaction, in order to avoid a pyrolytic gas-phase reaction, Ar purge time between the introduction of precursors is a key factor. For our reaction chamber, the purge time should be longer than 15 s and the corresponding growth rate is 2.2 Å/cycle.
Activated Kinetics of Room-Temperature-Deposited SrTiO3 Thin Films Investigated by Reflection-High-Energy-Electron-Diffraction-Monitored Annealing at Different Heating Rates
Authors: Wang Te-Chun , Lee Jung-Yuee , Hsieh Chih-Chang , Juang Jenh-Yih , Wu Kaung-Hsiung , Uen Tzeng-Ming , Gou Yih-Shun
Published: July 2005

A series of reflection-high-energy-electron-diffraction-monitored annealings with different heating rates have been conducted on Strontium Titanate films deposited by laser ablation at room temperature. All the films exhibited a steep RHEED intensity rise above 660°C during annealing with increasing temperature. The peak temperatures of the intensity derivatives were found to shift at different heating rates, suggesting an activated surface state transition. A Kissinger type plot of the peak temperatures showed an effective activation energy of 4 eV.
Simulation Study on Influence of Chemically Eroded Carbon Impurity Transport on Net Sputtering Erosion of Carbon Materials Exposed to Edge Fusion Plasmas
Authors: Kawakami Retsuo
Published: July 2005

Regarding TEXTOR and ITER-FEAT fusion devices, the net sputtering erosion rate of C targets exposed to their edge fusion plasmas has been investigated using a simulation code for plasma surface interactions, EDDY. The influence of the transport of chemically eroded CD4 molecules on the net erosion rate is presented. Emphasis is put on the difference in the simulated results between the CD4 reaction chain with e-, the CD4 reaction chain with e- plus D+, and the sticking coefficients of CD
x
locally returned back to the targets, which are related closely to the local redeposition, for a variety of plasma densities and temperatures. In particular, at a high density such as 1019 m-3 and low temperatures of less than 10 eV, the net erosion rate is found to be suppressed by a significant contribution of the local redeposition resulting from the charge exchange reactions of CD
x
with D+ if all the locally returned CD
x
radicals stick. For the ITER-FEAT divertor plasma, the profile of the net erosion rate along the outer vertical target is significantly changed by the C impurity concentration in the plasma, which is eroded from other wall surfaces and then transported by the plasma. For the D+ plasma exposure only, the net erosion rate is highest around the separatrix strike point. On the other hand, it is highest at the private plasma region if a few percent of the C impurity concentration is added to the D+ plasma exposure. The local redeposition resulting from the charge exchange reactions significantly suppresses the net erosion rates at these plasma regions, but does not bring about a significant change in the erosion/deposition profile along the outer vertical target.
Properties and Applications of a Modified Dielectric Barrier Discharge Generated at Atmospheric Pressure
Authors: Lee Yong-Hyuk , Yeom Geun-Young
Published: July 2005

An atmospheric pressure plasma was generated using a modified dielectric barrier discharge with the power electrode composed of multi-pins (i.e., a pin-to-plate type) instead of a conventional blank plate (i.e., a DBD-type), and the discharge and the photoresist etching characteristics were compared with those produced by the DBD-type at various He/O2mixtures. The pin-to-plate type showed a higher discharge current and a higher power consumption than the DBD-type at a given voltage. Therefore, the pin-to-plate type appeared to be more efficient than the conventional DBD-type. In addition, when the photoresist etch rate was examined, the pin-to-plate showed higher etch rates than the DBD-type at various He/O2mixtures. For the He/O2mixture, both types showed the maximum photoresist etch rate at a certain He/O2mixture. Using a gas mixture of 3 slm of O2and 10 slm of He, a maximum photoresist etch rate of 340 nm/min and 260 nm/min could be obtained using the pin-to-plate type and the DBD-type, respectively, at 10 kV AC for an electrode size of 500 mm×50 mm. No physical damage was observed on the metal lines of the TFT-LCD devices after photoresist etching under the above conditions.