bluuebunny/crossref_metadata_2025 huggingface dataset:
An Archaeal Chromosomal Autonomously Replicating Sequence Element from an Extreme Halophile,Halobacteriumsp. Strain NRC-1
Authors: Berquist Brian R. , DasSarma Shiladitya
Published: October 2003

We report on the identification and first cloning of an autonomously replicating sequence element from the chromosome of an archaeon, the extreme halophileHalobacteriumstrain NRC-1. The putative replication origin was identified by association with theorc7gene and replication ability in the host strain, demonstrated by cloning into a nonreplicating plasmid. Deletion analysis showed that sequences located up to 750 bp upstream of theorc7gene translational start, plus theorc7gene and 50 bp downstream, are sufficient to endow the plasmid with replication ability, as judged by expression of a plasmid-encoded mevinolin resistance selectable marker and plasmid recovery after transformation. Sequences located proximal to the two other chromosomally carried haloarchaealorcgenes (orc6andorc8) are not able to promote efficient autonomous replication. Located within the 750-bp region upstream oforc7is a nearly perfect inverted repeat of 31 bp, which flanks an extremely AT-rich (44%) stretch of 189 bp. The replication ability of the plasmid was lost when one copy of the inverted repeat was deleted. Additionally, the inverted repeat structure nearorc7homologs in the genomic sequences of two other halophiles,Haloarcula marismortuiandHaloferax volcanii, is highly conserved. Our results indicate that, in halophilic archaea, a chromosomal origin of replication is physically linked toorc7homologs and that this element is sufficient to promote autonomous replication. We discuss the finding of a functional haloarchaeal origin in relation to the large number oforc1-cdc6homologs identified in the genomes of all haloarchaea to date.
ThesloABCROperon ofStreptococcus mutansEncodes an Mn and Fe Transport System Required for Endocarditis Virulence and Its Mn-Dependent Repressor
Authors: Paik Sehmi , Brown Arunsri , Munro Cindy L. , Cornelissen Cynthia Nau , Kitten Todd
Published: October 2003

Streptococcus mutansbelongs to the viridans group of oral streptococci, which is the leading cause of endocarditis in humans. The LraI family of lipoproteins in viridans group streptococci and other bacteria have been shown to function as virulence factors, adhesins, or ABC-type metal transporters. We previously reported the identification of theS. mutansLraI operon,sloABCR, which encodes components of a putative metal uptake system composed of SloA, an ATP-binding protein, SloB, an integral membrane protein, and SloC, a solute-binding lipoprotein, as well as a metal-dependent regulator, SloR. We report here the functional analysis of this operon. By Western blotting, addition of Mn to the growth medium repressed SloC expression in a wild-type strain but not in asloRmutant. Other metals tested had little effect. Cells were also tested for aerobic growth in media stripped of metals then reconstituted with Mg and either Mn or Fe. Fe at 10 μM supported growth of the wild-type strain but not of asloAorsloCmutant. Mn at 0.1 μM supported growth of the wild-type strain andsloRmutant but not ofsloAorsloCmutants. The combined results suggest that the SloABC proteins transport both metals, although the SloR protein represses this system only in response to Mn. These conclusions are supported by55Fe uptake studies with Mn as a competitor. Finally, asloAmutant demonstrated loss of virulence in a rat model of endocarditis, suggesting that metal transport is required for endocarditis pathogenesis.
Mechanism ofPseudomonas aeruginosaRhlR Transcriptional Regulation of therhlABPromoter
Authors: Medina Gerardo , Juárez Katy , Valderrama Brenda , Soberón-Chávez Gloria
Published: October 2003

Pseudomonas aeruginosacontains two transcription regulators (LasR and RhlR) that, when complexed with their specific autoinducers (3-oxo-dodecanoyl-homoserine lactone and butanoyl-homoserine lactone, respectively) activate transcription of different virulence-associated traits. We studied the RhlR-dependent transcriptional regulation of therhlABoperon encoding rhamnosyltransferase 1, an enzyme involved in the synthesis of the surfactant monorhamnolipid, and showed that RhlR binds to a specific sequence in therhlABregulatory region, both in the presence and in the absence of its autoinducer. Our data suggest that in the former case it activates transcription, whereas in the latter it acts as a transcriptional repressor of this promoter. RhlR seems to repress the transcription of other quorum-sensing-regulated genes; thus, RhlR repressor activity might be of importance in the finely regulated expression ofP. aeruginosavirulence-associated traits.
Constitutive Activation of the
Escherichia coli
Pho Regulon Upregulates
rpoS
Translation in an Hfq-Dependent Fashion
Authors: Ruiz Natividad , Silhavy Thomas J.
Published: October 2003

Regulation of the σ factor RpoS occurs at the levels of transcription, translation, and protein stability activity, and it determines whether
Escherichia coli
turns on or off the stationary-phase response. To better understand the regulation of RpoS, we conducted genetic screens and found that mutations in the
pst
locus cause accumulation of RpoS during exponential growth. The
pst
locus encodes for the components of the high-affinity transport system for inorganic phosphate (P
i
), which is involved in sensing P
i
levels in the environment. When the Pst transporter is compromised (either by mutation or by P
i
starvation), the two-component system PhoBR activates the transcription of the Pho regulon, a subset of genes that encode proteins for transporting and metabolizing alternative phosphate sources. Our data show that strains carrying mutations which constitutively activate the Pho regulon have increased
rpoS
translation during exponential growth. This upregulation of
rpoS
translation is Hfq dependent, suggesting the involvement of a small regulatory RNA (sRNA). The transcription of this yet-to-be-identified sRNA is regulated by the PhoBR two-component system.
Transcription Regulation by Tandem-Bound FNR at
Escherichia coli
Promoters
Authors: Barnard Anne M. L. , Green Jeffrey , Busby Stephen J. W.
Published: October 2003

FNR is an
Escherichia coli
transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based on the
melR
promoter, in which a consensus FNR binding site was centered at position −41.5 relative to the transcription start site. A second consensus FNR binding site was introduced at different upstream locations, and promoter activity was assayed in vivo. FNR can activate transcription from these promoters when the upstream FNR binding site is located at many different positions. However, sharp repression is observed when the upstream-bound FNR is located near positions −85 or −95. This repression is relieved by the FNR G74C substitution mutant, previously identified as being defective in transcription repression at the
yfiD
promoter. A parallel series of artificial FNR-dependent promoters, carrying a consensus FNR binding site at position −61.5 and a second upstream DNA site for FNR, was also constructed. Again, promoter activity was repressed by FNR when the upstream-bound FNR was located at particular positions.
Characterization of the Two
Mycobacterium tuberculosis recA
Promoters
Authors: Gopaul Krishna K. , Brooks Patricia C. , Prost Jean-François , Davis Elaine O.
Published: October 2003

The
recA
gene of
Mycobacterium tuberculosis
is unusual in that it is expressed from two promoters, one of which, P1, is DNA damage inducible independently of LexA and RecA, while the other, P2, is regulated by LexA in the classical way (E. O. Davis, B. Springer, K. K. Gopaul, K. G. Papavinasasundaram, P. Sander, and E. C. Böttger, Mol. Microbiol. 46:791-800, 2002). In this study we characterized these two promoters in more detail. Firstly, we localized the promoter elements for each of the promoters, and in so doing we identified a mutation in each promoter which eliminates promoter activity. Interestingly, a motif with similarity to
Escherichia coli
σ
70
−35 elements but located much closer to the −10 element is important for optimal expression of P1, whereas the sequence at the −35 location is not. Secondly, we found that the sequences flanking the promoters can have a profound effect on the expression level directed by each of the promoters. Finally, we examined the contribution of each of the promoters to
recA
expression and compared their kinetics of induction following DNA damage.
Rgg Coordinates Virulence Factor Synthesis and Metabolism inStreptococcus pyogenes
Authors: Chaussee Michael S. , Somerville Greg A. , Reitzer Larry , Musser James M.
Published: October 2003

Streptococcus pyogenesis a human-specific pathogen that relies on its host for metabolic substrates. Rgg-like proteins constitute a family of transcriptional regulators present in several gram-positive bacteria. InS. pyogenes, Rgg influences the expression of several virulence-associated proteins localized to the cell wall and extracellular environment. Secreted enzymes may degrade host macromolecules, thereby liberating metabolic substrates. To determine if Rgg regulation of exoprotein expression is associated with altered metabolism, the catabolic activities ofS. pyogenesstrain NZ131 (serotype M49) and an isogenicrggmutant strain were analyzed during growth with complex and defined media. As expected, the wild-type strain preferentially used glucose and produced lactic acid during the exponential phase of growth. In contrast, therggmutant fermented arginine in the exponential phase of growth, even in the presence of glucose. Arginine degradation was associated with a neutral culture pH and excretion of NH3and ornithine. Arginine, serine, and asparagine were depleted from mutant cultures during growth. The addition of arginine and serine to culture media increased the growth yield and NH3production of mutant but not wild-type cultures. Addition of asparagine had no effect on the growth yield of either strain. Altered metabolism of arginine and serine in the mutant was associated with increased transcript levels of genes encoding arginine deiminase and a putative serine dehydratase. Thus, Rgg coordinates virulence factor synthesis and catabolic activity and may be important in the pathogen's adaptation to changes in the availability of metabolic substrates.
The Iron-Responsive Regulator Fur Is Transcriptionally Autoregulated and Not Essential inNeisseria meningitidis
Authors: Delany Isabel , Ieva Raffaele , Alaimo Cristina , Rappuoli Rino , Scarlato Vincenzo
Published: October 2003

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. Thefurgene inNeisseria meningitidishas been described as an essential gene that may regulate a broad array of genes. We succeeded in obtaining anN. meningitidismutant with thefurgene knocked out and used it to undertake studies offur-mediated iron regulation. We show that expression of both Fur and the transferrin binding protein Tbp2 is iron regulated and demonstrate that this regulation is Fur mediated for the Tbp2 protein. Footprinting analysis revealed that Fur binds to two distinct sites upstream of its coding region with different affinities and that these binding sites overlap two promoters that differentially control transcription of thefurgene in response to iron. The presence of two independently regulatedfurpromoters may allow meningococcus to fine-tune expression of this regulator controlling iron homeostasis, possibly during infection.
Regulation of Expression of the 2-Deoxy-
d
-Ribose Utilization Regulon,
deoQKPX
, from
Salmonella enterica
Serovar Typhimurium
Authors: Christensen Mette , Borza Tudor , Dandanell Gert , Gilles Anne-Marie , Barzu Octavian , Kelln Rod A. , Neuhard Jan
Published: October 2003

Salmonella enterica
, in contrast to
Escherichia coli
K12, can use 2-deoxy-
d
-ribose as the sole carbon source. The genetic determinants for this capacity in
S. enterica
serovar Typhimurium include four genes, of which three,
deoK
,
deoP
, and
deoX
, constitute an operon. The fourth,
deoQ
, is transcribed in the opposite direction. The
deoK
gene encodes deoxyribokinase. In silico analyses indicated that
deoP
encodes a permease and
deoQ
encodes a regulatory protein of the
deoR
family. The
deoX
gene product showed no match to known proteins in the databases. Deletion analyses showed that both a functional
deoP
gene and a functional
deoX
gene were required for optimal utilization of deoxyribose. Using gene fusion technology, we observed that
deoQ
and the
deoKPX
operon were transcribed from divergent promoters located in the 324-bp intercistronic region between
deoQ
and
deoK
. The
deoKPX
promoter was 10-fold stronger than the
deoQ
promoter, and expression was negatively regulated by DeoQ as well as by DeoR, the repressor of the deoxynucleoside catabolism operon. Transcription of
deoKPX
but not of
deoQ
was regulated by catabolite repression. Primer extension analysis identified the transcriptional start points of both promoters and showed that induction by deoxyribose occurred at the level of transcription initiation. Gel retardation experiments with purified DeoQ illustrated that it binds independently to tandem operator sites within the
deoQ
and
deoK
promoter regions with

K
d

values of 54 and 2.4 nM, respectively.
A Second PDZ-Containing Serine Protease Contributes to Activation of the Sporulation Transcription Factor σKinBacillus subtilis
Authors: Pan Qi , Losick Richard , Rudner David Z.
Published: October 2003

Gene expression late during the process of sporulation inBacillus subtilisis governed by a multistep, signal transduction pathway involving the transcription factor σK, which is derived by regulated proteolysis from the inactive proprotein pro-σK. Processing of pro-σKis triggered by a signaling protein known as SpoIVB, a serine protease that contains a region with similarity to the PDZ family of protein-protein interaction domains. Here we report the discovery of a second PDZ-containing serine protease called CtpB that contributes to the activation of the pro-σKprocessing pathway. CtpB is a sporulation-specific, carboxyl-terminal processing protease and shares several features with SpoIVB. We propose that CtpB acts to fine-tune the regulation of pro-σKprocessing, and we discuss possible models by which CtpB influences the σKactivation pathway.
Positive Correlation between Tyrosine Phosphorylation of CpsD and Capsular Polysaccharide Production inStreptococcus pneumoniae
Authors: Bender Matthew H. , Cartee Robert T. , Yother Janet
Published: October 2003

CpsA, CpsB, CpsC, and CpsD are part of a tyrosine phosphorylation regulatory system involved in modulation of capsule synthesis inStreptococcus pneumoniaeand many other gram-positive and gram-negative bacteria. Using an immunoblotting technique, we observed distinct laddering patterns ofS. pneumoniaecapsular polysaccharides of various serotypes and found that transfer of the polymer from the membrane to the cell wall was independent of size. Deletion ofcps2A,cps2B,cps2C, orcps2Din the serotype 2 strain D39 did not affect the ability to transfer capsule to the cell wall. Deletion ofcps2Corcps2D, which encode two domains of an autophosphorylating tyrosine kinase, resulted in the production of only short-chain polymers. The function of Cps2A is unknown, and the polymer laddering pattern of thecps2Adeletion mutants appeared similar to that of the parent, although the total amount of capsule was decreased. Loss of Cps2B, a tyrosine phosphatase and a kinase inhibitor, resulted in an increase in capsule amount and a normal ladder pattern. However, Cps2B mutants exhibited reduced virulence following intravenous inoculation of mice and were unable to colonize the nasopharynx, suggesting a diminished capacity to sense or respond to these environments. In D39 and its isogenic mutants, the amounts of capsule and tyrosine-phosphorylated Cps2D (Cps2D∼P) correlated directly. In contrast, restoration of type 2 capsule production followed by deletion ofcps2Bin Rx1, a laboratory passaged D39 derivative containing multiple uncharacterized mutations, resulted in decreased capsule amounts but no alteration in Cps2D∼P levels. Thus, a factor outside the capsule locus, which is either missing or defective in the Rx1 background, is important in the control of capsule synthesis.
Regulation of Expression of Cellulosomal Cellulase and Hemicellulase Genes in
Clostridium cellulovorans
Authors: Han Sung Ok , Yukawa Hideaki , Inui Masayuki , Doi Roy H.
Published: October 2003

The regulation of expression of the genes encoding the cellulases and hemicellulases of
Clostridium cellulovorans
was studied at the mRNA level with cells grown under various culture conditions. A basic pattern of gene expression and of relative expression levels was obtained from cells grown in media containing poly-, di- or monomeric sugars. The cellulase (
cbpA
and
engE
) and hemicellulase (
xynA
) genes were coordinately expressed in medium containing cellobiose or cellulose. Growth in the presence of cellulose, xylan, and pectin gave rise to abundant expression of most genes (
cbpA
-
exgS
,
engH
,
hbpA
,
manA
,
engM
,
engE
,
xynA
, and/or
pelA
) studied. Moderate expression of
cbpA
,
engH
,
manA
,
engE
, and
xynA
was observed when cellobiose or fructose was used as the carbon source. Low levels of mRNA from
cbpA
,
manA
,
engE
, and
xynA
were observed with cells grown in lactose, mannose, and locust bean gum, and very little or no expression of
cbpA
,
engH
,
manA
,
engE
, and
xynA
was detected in glucose-, galactose-, maltose-, and sucrose-grown cells. The
cbpA
-
exgS
and
engE
genes were most frequently expressed under all conditions studied, whereas expression of
xynA
and
pelA
was more specifically induced at higher levels in xylan- or pectin-containing medium, respectively. Expression of the genes (
cbpA
,
hbpA
,
manA
,
engM
, and
engE
) was not observed in the presence of most soluble di- or monosaccharides such as glucose. These results support the hypotheses that there is coordinate expression of some cellulases and hemicellulases, that a catabolite repression type of mechanism regulates cellulase expression in rapidly growing cells, and that the presence of hemicelluloses has an effect on cellulose utilization by the cell.
Global Mutational Analysis of NtrC-Like Activators in
Myxococcus xanthus
: Identifying Activator Mutants Defective for Motility and Fruiting Body Development
Authors: Caberoy Nora B. , Welch Roy D. , Jakobsen Jimmy S. , Slater Steven C. , Garza Anthony G.
Published: October 2003

The multicellular developmental cycle of
Myxococcus xanthus
requires large-scale changes in gene transcription, and recent findings indicate that NtrC-like activators play a prominent role in regulating these changes. In this study, we made insertions in 28 uncharacterized
ntrC
-like activator (
nla
) genes and found that eight of these insertions cause developmental defects. Hence, these results are consistent with the idea that
M. xanthus
uses a series of different NtrC-like activators during fruiting body development. Four of the eight developmental mutants we identified have motility defects. The
nla1
,
nla19
, and
nla23
mutants show S-motility defects, while the
nla24
mutant shows defects in both S-motility and A-motility. During development, aggregation of the
nla1
,
nla19
, and
nla23
mutants is delayed slightly and the
nla24
mutant shows no signs of aggregation or sporulation. The
nla4
,
nla6
,
nla18
, and
nla28
mutants have no appreciable loss in motility, but they fail to aggregate and to sporulate normally. The
nla18
mutant belongs to a special class of developmental mutants whose defects can be rescued when they are codeveloped with wild-type cells, suggesting that
nla18
fails to produce a cell-cell signal required for development. The three remaining activator mutants,
nla4
,
nla6
, and
nla28
, appear to have complex developmental phenotypes that include deficiencies in cell-cell developmental signals.
Cryo-Transmission Electron Microscopy of Frozen-Hydrated Sections ofEscherichia coliandPseudomonas aeruginosa
Authors: Matias Valério R. F. , Al-Amoudi Ashraf , Dubochet Jacques , Beveridge Terry J.
Published: October 2003

High-pressure freezing ofEscherichia coliK-12 andPseudomonas aeruginosaPAO1 in the presence of cryoprotectants provided consistent vitrification of cells so that frozen-hydrated sections could be cut, providing ∼2-nm resolution of structure. The size and shape of the bacteria, as well as their surface and cytoplasmic constituents, were nicely preserved and compared well with other published high-resolution techniques. Cells possessed a rich cytoplasm containing a diffuse dispersion of ribosomes and genetic material. Close examination of cells revealed that the periplasmic space was compressed during cryosectioning, a finding which provided supporting evidence that this space is filled by a compressible gel. Since the outer membrane and peptidoglycan layer are bonded together via lipoproteins, the space between them (although still part of the periplasmic space) was not as compacted. Even when this cryosectioning compression was taken into account, there was still substantial variability in the width of the periplasmic space. It is possible that the protoplast has some capacity to float freely within the periplasm.
2-Oxoglutarate:NADP
+
Oxidoreductase in
Azoarcus evansii
: Properties and Function in Electron Transfer Reactions in Aromatic Ring Reduction
Authors: Ebenau-Jehle Christa , Boll Matthias , Fuchs Georg
Published: October 2003

The conversion of [
14
C]benzoyl-coenzyme A (CoA) to nonaromatic products in the denitrifying β-proteobacterium
Azoarcus evansii
grown anaerobically on benzoate was investigated. With cell extracts and 2-oxoglutarate as the electron donor, benzoyl-CoA reduction occurred at a rate of 10 to 15 nmol min
−1
mg
−1
. 2-Oxoglutarate could be replaced by dithionite (200% rate) and by NADPH (∼10% rate); in contrast NADH did not serve as an electron donor. Anaerobic growth on aromatic compounds induced 2-oxoglutarate:acceptor oxidoreductase (KGOR), which specifically reduced NADP
+
, and NADPH:acceptor oxidoreductase. KGOR was purified by a 76-fold enrichment. The enzyme had a molecular mass of 290 ± 20 kDa and was composed of three subunits of 63 (γ), 62 (α), and 37 (β) kDa in a 1:1:1 ratio, suggesting an (αβγ)
2
composition. The native enzyme contained Fe (24 mol/mol of enzyme), S (23 mol/mol), flavin adenine dinucleotide (FAD; 1.4 mol/mol), and thiamine diphosphate (0.95 mol/mol). KGOR from
A. evansii
was highly specific for 2-oxoglutarate as the electron donor and accepted both NADP
+
and oxidized viologens as electron acceptors; in contrast NAD
+
was not reduced. These results suggest that benzoyl-CoA reduction is coupled to the complete oxidation of the intermediate acetyl-CoA in the tricarboxylic acid cycle. Electrons generated by KGOR can be transferred to both oxidized ferredoxin and NADP
+
, depending on the cellular needs. N-terminal amino acid sequence analysis revealed that the open reading frames for the three subunits of KGOR are similar to three adjacently located open reading frames in
Bradyrhizobium japonicum
. We suggest that these genes code for a very similar three-subunit KGOR, which may play a role in nitrogen fixation. The α-subunit is supposed to harbor one FAD molecule, two [4Fe-4S] clusters, and the NADPH binding site; the β-subunit is supposed to harbor one thiamine diphosphate molecule and one further [4Fe-4S] cluster; and the γ-subunit is supposed to harbor the CoA binding site. This is the first study of an NADP
+
-specific KGOR. A similar NADP
+
-specific pyruvate oxidoreductase, which contains all domains in one large subunit, has been reported for the mitochondrion of the protist
Euglena gracilis
and the apicomplexan
Cryptosporidium parvum
.
Molecular Characterization of
Brucella abortus
Chromosome II Recombination
Authors: Tsoktouridis Georgios , Merz Christian A. , Manning Simon P. , Giovagnoli-Kurtz Renée , Williams Leanne E. , Mujer Cesar V. , Hagius Sue , Elzer Philip , Redkar Rajendra J. , Patra Guy , DelVecchio Vito G.
Published: October 2003

Large-scale genomic rearrangements including inversions, deletions, and duplications are significant in bacterial evolution. The recently completed
Brucella melitensis
16M and
Brucella suis
1330 genomes have facilitated the investigation of such events in the
Brucella
spp. Suppressive subtractive hybridization (SSH) was employed in identifying genomic differences between
B. melitensis
16M and
Brucella abortus
2308. Analysis of 45 SSH clones revealed several deletions on chromosomes of
B. abortus
and
B. melitensis
that encoded proteins of various metabolic pathways. A 640-kb inversion on chromosome II of
B. abortus
has been reported previously (S. Michaux Charachon, G. Bourg, E. Jumas Bilak, P. Guigue Talet, A. Allardet Servent, D. O'Callaghan, and M. Ramuz, J. Bacteriol.
179:
3244-3249, 1997) and is further described in this study. One end of the inverted region is located on a deleted TATGC site between open reading frames BMEII0292 and BMEII0293. The other end inserted at a GTGTC site of the cyclic-di-GMP phosphodiesterase A (PDEA) gene (BMEII1009), dividing PDEA into two unequal DNA segments of 160 and 977 bp. As a consequence of inversion, the 160-bp segment that encodes the N-terminal region of PDEA was relocated at the opposite end of the inverted chromosomal region. The splitting of the PDEA gene most likely inactivated the function of this enzyme. A recombination mechanism responsible for this inversion is proposed.
ATP-Bound Conformation of Topoisomerase IV: a Possible Target for Quinolones in
Streptococcus pneumoniae
Authors: Sifaoui Farid , Lamour Valérie , Varon Emmanuelle , Moras Dino , Gutmann Laurent
Published: October 2003

Topoisomerase IV, a C
2
E
2
tetramer, is involved in the topological changes of DNA during replication. This enzyme is the target of antibacterial compounds, such as the coumarins, which target the ATP binding site in the ParE subunit, and the quinolones, which bind, outside the active site, to the quinolone resistance-determining region (QRDR). After site-directed and random mutagenesis, we found some mutations in the ATP binding site of ParE near the dimeric interface and outside the QRDR that conferred quinolone resistance to
Streptococcus pneumoniae
, a bacterial pathogen. Modeling of the N-terminal, 43-kDa ParE domain of
S. pneumoniae
revealed that the most frequent mutations affected conserved residues, among them His43 and His103, which are involved in the hydrogen bond network supporting ATP hydrolysis, and Met31, at the dimeric interface. All mutants showed a particular phenotype of resistance to fluoroquinolones and an increase in susceptibility to novobiocin. All mutations in ParE resulted in resistance only when associated with a mutation in the QRDR of the GyrA subunit. Our models of the closed and open conformations of the active site indicate that quinolones preferentially target topoisomerase IV of
S. pneumoniae
in its ATP-bound closed conformation.
Identification of Three New Genes Involved in Morphogenesis and Antibiotic Production inStreptomyces coelicolor
Authors: Sprusansky Ondrej , Zhou Liqin , Jordan Sarah , White Jared , Westpheling Janet
Published: October 2003

We report the isolation and partial characterization of three new mutants ofStreptomyces coelicolorthat are defective in morphogenesis and antibiotic production. The genes identified by the mutations were located and cloned by using a combination of Tn5in vitro mutagenesis, cotransformation, and genetic complementation. Mutant SE69 produces lower amounts of antibiotics than the wild type produces, produces spores only after prolonged incubation on rich media, and identifies a gene whose predicted protein product is similar to the GntR family of transcriptional regulators; also, production of aerial mycelia on both rich and poor media is significantly delayed in this mutant. Mutant SE293 is defective in morphogenesis, overproduces antibiotics on rich media, fails to grow on minimal media, and identifies a gene whose predicted protein product is similar to the TetR family of transcriptional regulators. Preliminary evidence suggests that the SE293 gene product may control a molybdopterin binding protein located immediately adjacent to it. Mutant SJ175 sporulates sooner and more abundantly than the wild type and overproduces antibiotics on rich media, and it identifies a gene whose predicted protein product contains regions of predominantly hydrophobic residues similar to those of integral membrane proteins.
Interfering with Different Steps of Protein SynthesisExplored by Transcriptional Profiling of
Escherichia coli
K-12
Authors: Sabina Jeffrey , Dover Nir , Templeton Lori J. , Smulski Dana R. , Söll Dieter , LaRossa Robert A.
Published: October 2003

Escherichia
coli
responses to four inhibitors that interfere with translation
were monitored at the transcriptional level. A DNA microarray method
provided a comprehensive view of changes in mRNA levels after exposure
to these agents. Real-time reverse transcriptase PCRanalysis served to verify observations made with microarrays, and a
chromosomal
grpE
::
lux
operon
fusion was employed to specifically monitor the heat shock response.
4-Azaleucine, a competitive inhibitor of leucyl-tRNA synthetase,
surprisingly triggered the heat shock response. Administration of
mupirocin, an inhibitor of isoleucyl-tRNA synthetase activity, resulted
in changes reminiscent of the stringent response. Treatment with
kasugamycin and puromycin (targeting ribosomal subunit association as
well as its peptidyl-transferase activity) caused accumulation of mRNAs
from ribosomal protein operons. Abundant biosynthetic transcripts were
often significantly diminished after treatment with any of these
agents. Exposure of a
relA
strain to mupirocin resulted in
accumulation of ribosomal protein operon transcripts. However, the
relA
strain's response to the other inhibitors was quite
similar to that of the wild-type
strain.
A Second and Unusual
pucBA
Operon of
Rhodobacter sphaeroides
2.4.1: Genetics and Function of the Encoded Polypeptides
Authors: Zeng Xiaohua , Choudhary Madhu , Kaplan Samuel
Published: October 2003

A new operon (designated the
puc2BA
operon) displaying a high degree of similarity to the original
pucBA
genes of
Rhodobacter sphaeroides
2.4.1 (designated
puc1
) was identified and studied genetically and biochemically. The
puc2B
-encoded polypeptide is predicted to exhibit 94% identity with the original β-apoprotein. The
puc2A
-encoded polypeptide is predicted to be much larger (263 amino acids) than the 54-amino-acid
puc1A
-encoded polypeptide. In the first 48 amino acids of the
puc2A
-encoded polypeptide there is 58% amino acid sequence identity to the original
puc1A
-encoded polypeptide. We found that
puc2BA
is expressed, and DNA sequence data suggested that
puc2BA
is regulated by the PpsR/AppA repressor-antirepressor and FnrL. Employing genetic and biochemical approaches, we obtained evidence that the
puc2B
-encoded polypeptide is able to enter into LH2 complex formation, but neither the full-length
puc2A
-encoded polypeptide nor its N-terminal 48-amino-acid derivative is able to enter into LH2 complex formation. Thus, the sole source of α-polypeptides for the LH2 complex is
puc1A
. The role of the
puc1C
-encoded polypeptide was also determined. We found that the presence of this polypeptide is essential for normal levels of transcription and translation of the
puc1
operon but not for transcription and translation of the
puc2
operon. Thus, the
puc1C
gene product appears to have both transcriptional and posttranscriptional roles in LH2 formation. Finally, the absence of any LH2 complex when
puc1B
was deleted in frame was surprising since we know that in the presence of functional
puc2BA
, approximately 30% of the LH2 complexes normally observed contain a
puc2B
-encoded β-polypeptide.
Changes inEscherichia colirRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis
Authors: Schneider David A. , Gourse Richard L.
Published: October 2003

rRNA synthesis is the rate-limiting step in ribosome synthesis inEscherichia coli. Its regulation has been described in terms of a negative-feedback control loop in which rRNA promoter activity responds to the amount of translation. The feedback nature of this control system was demonstrated previously by artificially changing ribosome synthesis rates and observing responses of rRNA promoters. However, it has not been demonstrated previously that the initiating nucleoside triphosphate (iNTP) and guanosine 5′-diphosphate 3′-diphosphate (ppGpp), the molecular effectors responsible for controlling rRNA promoters in response to changes in the nutritional environment, are responsible for altering rRNA promoter activities under these feedback conditions. Here, we show that most feedback situations result in changes in the concentrations of both the iNTP and ppGpp and that the directions of these changes are consistent with a role for these two small-molecule regulators in feedback control of rRNA synthesis. In contrast, we observed no change in the level of DNA supercoiling under the feedback conditions examined.
Reduced Water Availability Influences the Dynamics, Development, and Ultrastructural Properties of
Pseudomonas putida
Biofilms
Authors: Chang Woo-Suk , Halverson Larry J.
Published: October 2003

Pseudomonas putida
strain mt-2 unsaturated biofilm formation proceeds through three distinct developmental phases, culminating in the formation of a microcolony. The form and severity of reduced water availability alter cell morphology, which influences microcolony size and ultrastructure. The dehydration (matric stress) treatments resulted in biofilms comprised of smaller cells, but they were taller and more porous and had a thicker extracellular polysaccharide layer at the air interface. In the solute stress treatments, cell filamentation occurred more frequently in the presence of high concentrations of ionic (but not nonionic) solutes, and these filamented cells drastically altered the biofilm architecture.
Characterization of
divIVA
and Other Genes Located in the Chromosomal Region Downstream of the
dcw
Cluster in
Streptococcus pneumoniae
Authors: Fadda Daniela , Pischedda Carla , Caldara Fabrizio , Whalen Michael B. , Anderluzzi Daniela , Domenici Enrico , Massidda Orietta
Published: October 2003

We analyzed the chromosome region of
Streptococcus pneumoniae
located downstream of the division and cell wall (
dcw
) cluster that contains the homolog of the
Bacillus subtilis
cell division gene
divIVA
and some genes of unknown function. Inactivation of
divIVA
in
S. pneumoniae
resulted in severe growth inhibition and defects in cell shape, nucleoid segregation, and cell division. Inactivation of the
ylm
genes resulted in some morphological and/or division abnormalities, depending on the inactivated gene. Transcriptional analysis revealed a relationship between these genes and the
ftsA
and
ftsZ
cell division genes, also indicating that the connection between the
dcw
cluster and the
divIVA
region is more extensive than just chromosomal position and gene organization.
Metagenomic Analyses of an Uncultured Viral Community from Human Feces
Authors: Breitbart Mya , Hewson Ian , Felts Ben , Mahaffy Joseph M. , Nulton James , Salamon Peter , Rohwer Forest
Published: October 2003

Here we present the first metagenomic analyses of an uncultured viral community from human feces, using partial shotgun sequencing. Most of the sequences were unrelated to anything previously reported. The recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes.
Noncommutativity and Its Freedoms Due to the pp-Wave and Background Gauge Fields
Authors: Kamani Davoud
Published: October 2003

In this paper we consider an open string attached to a Dp-brane, in the presence of the pp-wave and background gauge fields. The effects of the string mass on the open string propagator, open string metric and the noncommutativity parameter are studied. Some free matrices appear in the propagator and in the open string variables. The symmetries of the string propagator and consistency with the zero mass case put some restrictions on these matrices.
Brane Inflation from Rotation of D4 Brane
Authors: Piao Yun-Song , Zhang Xinmin , Zhang Yuan-Zhong
Published: October 2003

In this paper, an inflationary model from the rotation of D4-brane is constructed. We show that for a very wide range of parameter, this model satisfies the observation. Our model offers a new avenue for brane inflation.
SU(2) Chiral Sigma Model Study of Phase Transition in Hybrid Stars
Authors: Jena P. K. , Singh L. P.
Published: October 2003

We use a modified SU(2) chiral sigma model to study nuclear matter component and simple bag model for quark matter constituting a neutron star. We also study the phase transition of nuclear matter to quark matter with the mixed phase characterized by two conserved charges in the interior of highly dense neutron stars. Stable solutions of Tolman–Oppenheimer–Volkoff equations representing hybrid stars are obtained with a maximum mass of 1.67M⊙ and radius around 8.9 km.
Induced Gauge Structure for the Zero Modes of Two-Dimensional Solitons
Authors: Igarashi Yuji , Kitakado Shinsaku , Otsu Hideharu , Sato Toshiro
Published: October 2003

The induced gauge structure for the zero modes of two-dimensional solitons is considered bearing in mind the possibility of finding the origin of gauge fields in field theory.
Generalized Toda Theories from WZNW Reduction
Authors: Wyllard Niclas
Published: October 2003

We reconsider the recently proposed generalized Toda field theories using the framework of WZNW → Toda reduction. In particular, we study the general [Formula: see text] algebra associated with the generalized models and derive a closed expression for the [Formula: see text] algebra bracket. A free field realization of the general W algebra is also presented. All results apply also to the case of ordinary Toda theories.
A Yang–Mills Theory in Loop Space and Chapline–Manton Coupling
Authors: Deguchi Shinichi , Nakajima Tadahito
Published: October 2003

We consider a Yang–Mills theory in loop space with the affine gauge group. From this theory, we derive a local field theory with Yang–Mills fields and Abelian antisymmetric and symmetric tensor fields of the second rank. The Chapline–Manton coupling, i.e. coupling of Yang–Mills fields and a second-rank antisymmetric tensor field via the Chern–Simons three-form is obtained systematically.
Non-Relativistic Model for the Semileptonic Λb→Λc Decay
Authors: Chakraverty Debrupa , De Triptesh , Dutta-Roy Binayak , Gupta K. S.
Published: October 2003

We calculate the decay width for [Formula: see text] in the framework of a non-relativistic quark (NRQ) model of heavy baryons where the light quarks play the role of spectators. Our calculation does not make an explicit use of the heavy quark symmetry. The branching ratio for the above process as calculated here agrees reasonably well with the experimental value.
On Prospects for Exploration of Supersymmetry in Double Beta Decay Experiments
Authors: Bednyakov V. A , Brudanin V. B. , Kovalenko S. G. , Vylov Ts. D.
Published: October 2003

We analyze constraints on the parameters of the Rp violating supersymmetry ([Formula: see text] SUSY) which can be extracted from non-observation of the neutrinoless nuclear double beta decay (0νββ) at a given half-life lower bound. Our analysis covers a large class of phenomenologically viable [Formula: see text] SUSY models. We introduce special characteristics: the SUSY sensitivity of a ββ-decaying isotope and the SUSY reach of a 0νββ-experiment. The former provides a physical criterion for a selection of the most promising isotopes for SUSY searches and the latter gives a measure of success for a 0νββ-experiment in exploring the [Formula: see text] SUSY parameter space. On this basis we discuss prospects for exploration of supersymmetry in various 0νββ-experiments.
Minimization of the Scalar Potential in Softly Broken SU(2)×U(1)N=1 SYM with Higgs Matter
Authors: Kondrashuk I. N.
Published: October 2003

We consider a particular extension of the scalar two-Higgs potential of the Minimal Supersymmetric Standard Model to an arbitrary number of Higgs doublets. The extended potential has an absolute and only nontrivial minimum that is found exactly. It appears that this minimum is a simple analog to the well-known minimum of the MSSM. This result is applied to a low-energy Higgs potential of the finite Grand Unification Theory where six Higgs doublets are present.
Super High-Order Virasoro Gravity and High-Order Virasoro Topological Matter
Authors: Zha Chao-Zheng , Zhao Wei-Zhong
Published: October 2003

N=2 super high-order Virasoro algebra and topological high-order Virasoro algebra are constructed. We then present the super high-order Virasoro gravity and high-order Virasoro topological matter.
Energy Eigenvalues for a Class of One-Dimensional Potentials via Quantum Hamilton–Jacobi Formalism
Authors: Bhalla R. S. , Kapoor A. K. , Panigrahi P. K.
Published: October 2003

Using quantum Hamilton–Jacobi formalism of Leacock and Padgett, we show how to obtain the known energy eigenvalues for a class of widely studied, solvable, one-dimensional potentials. An alternative method to the one given by us, is provided which unambiguously determines the quantum momentum function and hence the eigenvalues for these Hamiltonians.
$B_0\bar B_0$-Mixing Involving Supersymmetry
Authors: Urban J. , Krauss F. , Hofmann Ch. , Soff G.
Published: October 2003

We calculate all relevant Feynman-diagrams in lowest order for [Formula: see text]-mixing. We add to the Standard Model (SM) two scalar Higgs-doublets and take into account the Minimal Supersymmetric Standard Model (MSSM). Within the Standard Model which has been extended by two Higgs-doublets we find the following relation between the Higgs-mass and its vacuum expectation value (vev): mH=5000/7(au-0.43). Inclusion of the MSSM pushes the value of Vtd to the lower edge of the experimentally allowed range.
Notes on Axion, Inflation and Graceful Exit in Stringy Cosmology
Authors: Maharana Jnanadeva , Mukherji Sudipta , Panda Sudhakar
Published: October 2003

We study the classical equations of motion and the corresponding Wheeler–De Witt equations for tree level string effective action with dilaton and axion. The graceful exit problem in certain cases is then analyzed.
On the Generalized Statistics Through the Deformation of the Exterior Algebra
Authors: Daoud M. , Hassouni Y.
Published: October 2003

Using a consistent deformation of the exterior algebra, we propose a generalized statistic depending on the Braid operator allowing this deformation. The deformed Fock space is constructed and the structure of multiparticle wave functions is given.
UV-Regularization of Field Discontinuities
Authors: Sveshnikov K. , Silaev P. , Cherednikov I.
Published: October 2003

A nonperturbative regularization of uv-divergencies, caused by finite discontinuities in the field configuration, is discussed in the context of (1+1)-dimensional kink models. The relationship between this procedure and the appearance of "quantum copies" of classical kink solutions is studied in detail and confirmed by conventional methods of soliton quantization.
Test of the Isospin Invariance Using Polarization Effects in Slow Antiproton Annihilation, $\bar p+ p(n)\rightarrow P+V$
Authors: Yalçin C. , Rekalo M. P. , Koru H.
Published: October 2003

The spin structure of the amplitudes for antiproton annihilation at rest, [Formula: see text], P=π, η;V=ρ, ω, ϕ, is established. The relation between symmetry properties of strong interaction (isospin invariance and the invariance relative to charge conjugation) and the polarization effects in such reactions are derived. It is demonstrated that the simplest polarization effects in [Formula: see text], namely, the elements of V-meson density matrix, are sensitive to possible violation of the isospin invariance and C-invariance. The analysis of the spin structure of P-wave annihilation amplitudes is also presented.
Distorted Pion Wave Function in the Pionic Decay of the Lightest Λ Hypernuclei
Authors: Kelkar Neelima G.
Published: October 2003

The effect of pion distortions is studied in the π-mesonic decay [Formula: see text] of the lightest Λ hypernuclei. Reduction in the decay rates of both these nuclei is observed. This is in contrast to previous observations of enhancements in the decay rates of all nuclei ranging from [Formula: see text] to [Formula: see text]. The distorted wave function is evaluated using a theoretically deduced pion–nucleus optical potential. Calculations are also made using phenomenological optical potentials which fit the pion–nucleus scattering data quite well. Results with theoretical and phenomenological potentials are in fairly good agreement qualitatively, but the exact results are sensitive to the type of optical potential used.
On a Stringy Singular Cohomology
Authors: Hübsch Tristan
Published: October 2003

String theory has already motivated, suggested, and sometimes well-nigh proved a number of interesting and sometimes unexpected mathematical results, such as mirror symmetry. A careful examination of the behavior of string propagation on (mildly) singular varieties similarly suggests a new type of (co)homology theory. It has the "good behavior" of the well-established intersection (co)homology and L2-cohomology, but is markedly different in some aspects. For one, unlike the intersection (co)homology and the L2-cohomology (or any other known thus far), this new cohomology is symmetric with respect to the mirror map. Among the available choices, this makes it into a prime candidate for describing the string theory zero modes in geometrical terms.
Logarithmic Yangians in WZW Models
Authors: Bernard D. , Maassarani Z. , Mathieu P.
Published: October 2003

A new action of the Yangians in the WZW models is displayed. Its structure is generic and level-independent. This Yangian is the natural extension at the conformal point of the one unraveled in massive theories with current algebras. Hopefully, this new symmetry of WZW models will lead to a deeper understanding of the integrable structure of conformal field theories and their deformations.
Propagating Waves in an Extremal Black String
Authors: Lee H. W. , Myung Y. S. , Kim Jin Young , Park D. K.
Published: October 2003

We investigate the black string in the context of string theories. It is shown that the graviton is the only propagating mode in the (2+1)-dimensional extremal black string background. Both the dilaton and axion turn out to be non-propagating modes.
Higgs Boson Mass Bounds in the Standard and Minimal Supersymmetric Standard Model with Four Generations
Authors: Kang Sin Kyu , Park Gye T.
Published: October 2003

We study the question of distinguishability of the Higgs sector between the standard model with four generations (SM4) and the minimal supersymmetric standard model with four generations (MSSM4). We find that a gap exists between the SM4 and MSSM4 Higgs boson masses for a range of fourth generation fermion mass considered in the analysis at a fixed top quark mass. We also compare the Higgs boson mass bounds in these models with those in the standard and the minimal supersymmetric standard models.
Higher-Dimensional SUSY Quantum Mechanics
Authors: Das A. , Okubo S. , Pernice S. A.
Published: October 2003

Higher-dimensional supersymmetric quantum mechanics is studied. General properties of the two-dimensional case are presented. For three spatial dimensions or higher, a spin structure is shown to arise naturally from the nonrelativistic supersymmetry algebra.