bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative Control of Quorum Sensing by RpoN (σ54) inPseudomonas aeruginosaPAO1
Authors: Heurlier Karin , Dénervaud Valerie , Pessi Gabriella , Reimmann Cornelia , Haas Dieter 
Published: March 2003

ABSTRACTInPseudomonas aeruginosaPAO1, the expression of several virulence factors such as elastase, rhamnolipids, and hydrogen cyanide depends on quorum-sensing regulation, which involves thelasRIandrhlRIsystems controlled byN-(3-oxododecanoyl)-l-homoserine lactone andN-butyryl-l-homoserine lactone, respectively, as signal molecules. InrpoNmutants lacking the transcription factor σ54, the expression of thelasRandlasIgenes was elevated at low cell densities, whereas expression of therhlRandrhlIgenes was markedly enhanced throughout growth by comparison with the wild type and the complemented mutant strains. As a consequence, therpoNmutants had elevated levels of both signal molecules and overexpressed the biosynthetic genes for elastase, rhamnolipids, and hydrogen cyanide. The quorum-sensing regulatory protein QscR was not involved in the negative control exerted by RpoN. By contrast, in anrpoNmutant, the expression of thegacAglobal regulatory gene was significantly increased during the entire growth cycle, whereas another global regulatory gene,vfr, was downregulated at high cell densities. In conclusion, it appears that GacA levels play an important role, probably indirectly, in the RpoN-dependent modulation of the quorum-sensing machinery ofP. aeruginosa.
Differential Expression of the
Escherichia
coli
Autoaggregation Factor Antigen 43
Authors: Schembri Mark A. , Hjerrild Louise , Gjermansen Morten , Klemm Per 
Published: March 2003

ABSTRACT

Antigen 43 (Ag43) is a self-recognizing surface adhesin found in most
Escherichia
coli
strains. Due to its excellent cell-to-cell aggregation characteristics, Ag43 expression confers clumping and fluffing of cells and promotes biofilm formation. Ag43 expression is repressed by the cellular redox sensor OxyR. Here we used mutant versions of OxyR that are locked in either the reduced or the oxidized form as well as the addition of a simple redox-changing chemical to show that the redox state of OxyR influences Ag43 expression. Furthermore, the redox state of OxyR influences the biofilm-forming potential of
E
.
coli
. Finally, we demonstrated that Ag43-mediated cell aggregation confers significant protection against hydrogen peroxide killing.
The Ascorbate Transporter of
Escherichia coli
Authors: Zhang Zhongge , Aboulwafa Mohammad , Smith Meghan H. , Saier, Milton H. 
Published: March 2003

ABSTRACT

The
sgaTBA
genes of
Escherichia coli
encode a putative 12-transmembrane α-helical segment (12 TMS) transporter, an enzyme IIB-like protein and an enzyme IIA-like protein of the phosphotransferase system (PTS), respectively. We show that all three proteins as well as the energy-coupling PTS proteins, enzyme I and HPr, are required for the anaerobic utilization and uptake of
l
-ascorbate in vivo and its phosphoenolpyruvate-dependent phosphorylation in vitro. The transporter exhibits an apparent

K
m

for
l
-ascorbate of 9 μM and is highly specific. The
sgaTBA
genes are regulated at the transcriptional level by the
yjfQ
gene product, as well as by Crp and Fnr. The
yjfR
gene product is essential for
l
-ascorbate utilization and probably encodes a cytoplasmic
l
-ascorbate 6-phosphate lactonase. We conclude that SgaT represents a novel prototypical enzyme IIC that functions with SgaA and SgaB to allow phosphoryl transfer from HPr(his-P) to
l
-ascorbate via the phosphoryl transfer pathway: PEP → enzyme I-P → HPr-P → IIA-

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\stackrel{\mathrm{SgaA}}{\mathrm{P}}\) \end{document}

→ IIB-

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\stackrel{\mathrm{SgaB}}{\mathrm{P}}\) \end{document}

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\stackrel{\textstyle{\mathrm{IIC^{SgaT}}}}{{\rightarrow}}\) \end{document}

l
-ascorbate-6-P.
The
src
Homology 3-Like Domain of the Diphtheria Toxin Repressor (DtxR) Modulates Repressor Activation through Interaction with the Ancillary Metal Ion-Binding Site
Authors: Love John F. , vanderSpek Johanna C. , Murphy John R. 
Published: March 2003

ABSTRACT

The diphtheria toxin repressor (DtxR) is a transition metal ion-activated repressor that acts as a global regulatory element in the control of iron-sensitive genes in
Corynebacterium diphtheriae
. We recently described (L. Sun, J. C. vanderSpek, and J. R. Murphy, Proc. Natl. Acad. Sci. USA 95:14985-14990, 1998) the isolation and in vivo characterization of a hyperactive mutant of DtxR, DtxR(E175K), that appeared to be constitutively active. We demonstrate here that while DtxR(E175K) remains active in vivo in the presence of 300 μM 2,2′dipyridyl, the purified repressor is, in fact, dependent upon low levels of transition metal ion to transit from the inactive apo form to the active metal ion-bound form of the repressor. Binding studies using 8-anilino-1-naphthalenesulfonic acid suggest that the E175K mutation stabilizes an intermediate of the molten-globule form of the repressor, increasing exposure of hydrophobic residues to solvent. We demonstrate that the hyperactive DtxR(E175K) phenotype is dependent upon an intact ancillary metal ion-binding site (site 1) of the repressor. These observations support the hypothesis that metal ion binding in the ancillary site facilitates the conversion of the inactive apo-repressor to its active, operator-binding conformation. Furthermore, these results support the hypothesis that the C-terminal
src
homology 3-like domain of DtxR plays an active role in the modulation of repressor activity.
YscP and YscU Regulate Substrate Specificity of theYersiniaType III Secretion System
Authors: Edqvist Petra J. , Olsson Jan , Lavander Moa , Sundberg Lena , Forsberg Åke , Wolf-Watz Hans , Lloyd Scott A. 
Published: March 2003

ABSTRACTPathogenicYersiniaspecies use a type III secretion system to inhibit phagocytosis by eukaryotic cells. At 37°C, the secretion system is assembled, forming a needle-like structure on the bacterial cell surface. Upon eukaryotic cell contact, six effector proteins, called Yops, are translocated into the eukaryotic cell cytosol. Here, we show that ayscPmutant exports an increased amount of the needle component YscF to the bacterial cell surface but is unable to efficiently secrete effector Yops. Mutations in the cytoplasmic domain of the inner membrane protein YscU suppress theyscPphenotype by reducing the level of YscF secretion and increasing the level of Yop secretion. These results suggest that YscP and YscU coordinately regulate the substrate specificity of theYersiniatype III secretion system. Furthermore, we show that YscP and YscU act upstream of the cell contact sensor YopN as well as the inner gatekeeper LcrG in the pathway of substrate export regulation. These results further strengthen the strong evolutionary link between flagellar biosynthesis and type III synthesis.
Mutations Which Uncouple Transport and Phosphorylation in the
d
-Mannitol Phosphotransferase System of
Escherichia coli
K-12 and
Klebsiella pneumoniae
1033-5P14
Authors: Otte Susanne , Scholle Annette , Turgut Sevket , Lengeler Joseph W. 
Published: March 2003

ABSTRACT

Mutants of
Escherichia coli
K-12 were isolated which lack the normal phosphotransferase system-dependent catabolic pathway for
d
-mannitol (Mtl). In some mutants the
pts
genes for the general proteins enzyme I and histidine protein of the phosphoenolpyruvate-dependent carbohydrate phosphotransferase systems were deleted. Other mutants expressed truncated mannitol-specific enzymes II (II
Mtl
) which lacked the IIA
Mtl
or IIBA
Mtl
domain(s), and the
mtlA
genes originated either from
E. coli
K-12 or from
Klebsiella pneumoniae
1033-5P14. The
dalD
gene from
Klebsiella oxytoca
M5a1 was cloned on single-copy plasmids and transformed into the strains described above. This gene encodes an NAD-dependent
d
-arabinitol dehydrogenase (DalD) which converts
d
-arabinitol into
d
-xylulose and also converts
d
-mannitol into
d
-fructose. The different strains were used to isolate mutations which allow efficient transport of mannitol through the nonphosphorylated II
Mtl
complexes by selecting for growth on this polyhydric alcohol. More than 40 different mutants were analyzed to determine their ability to grow on mannitol, as well as their ability to bind and transport free mannitol and, after restoration of the missing domain(s), their ability to phosphorylate mannitol. Four mutations were identified (E218A, E218V, H256P, and H256Y); all of these mutations are located in the highly conserved loop 5 of the IIC membrane-bound transporter, and two are located in its GIHE motif. These mutations were found to affect the various functions in different ways. Interestingly, in the presence of all II
Mtl
variants, whether they were in the truncated form or in the complete form, in the phosphorylated form or in the nonphosphorylated form, and in the wild-type form or in the mutated form, growth occurred on the low-affinity analogue
d
-arabinitol with good efficiency, while only the uncoupled mutated forms transported mannitol at a high rate.
Characterization of a Novel Thermostable
O
-Acetylserine Sulfhydrylase from
Aeropyrum pernix
K1
Authors: Mino Koshiki , Ishikawa Kazuhiko 
Published: March 2003

ABSTRACT

An
O
-acetylserine sulfhydrylase (OASS) from the hyperthermophilic archaeon
Aeropyrum pernix
K1, which shares the pyridoxal 5′-phosphate binding motif with both OASS and cystathionine β-synthase (CBS), was cloned and expressed by using
Escherichia coli
Rosetta(DE3). The purified protein was a dimer and contained pyridoxal 5′-phosphate. It was shown to be an enzyme with CBS activity as well as OASS activity in vitro. The enzyme retained 90% of its activity after a 6-h incubation at 100°C. In the
O
-acetyl-
l
-serine sulfhydrylation reaction, it had a pH optimum of 6.7, apparent

K
m

values for
O
-acetyl-
l
-serine and sulfide of 28 and below 0.2 mM, respectively, and a rate constant of 202 s
−1
. In the
l
-cystathionine synthetic reaction, it showed a broad pH optimum in the range of 8.1 to 8.8, apparent

K
m

values for
l
-serine and
l
-homocysteine of 8 and 0.51 mM, respectively, and a rate constant of 0.7 s
−1
.
A. pernix
OASS has a high activity in the
l
-cysteine desulfurization reaction, which produces sulfide and
S
-(2,3-hydroxy-4-thiobutyl)-
l
-cysteine from
l
-cysteine and dithiothreitol.
TheMoraxella catarrhalisImmunoglobulin D-Binding Protein MID Has Conserved Sequences and Is Regulated by a Mechanism Corresponding to Phase Variation
Authors: Möllenkvist Andrea , Nordström Therése , Halldén Christer , Christensen Jens Jørgen , Forsgren Arne , Riesbeck Kristian 
Published: March 2003

ABSTRACTThe prevalence of theMoraxella catarrhalisimmunoglobulin D (IgD)-binding outer membrane protein MID and its gene was determined in 91 clinical isolates and in 7 culture collection strains. Eighty-four percent of the clinicalMoraxellastrains expressed MID-dependent IgD binding. Themidgene was detected in all strains as revealed by homology of the signal peptide sequence and a conserved area in the 3′ end of the gene. When MID proteins from five different strains were compared, an identity of 65.3 to 85.0% and a similarity of 71.2 to 89.1% were detected. Gene analyses showed several amino acid repeat motifs in the open reading frames, and MID could be called a putative autotransport protein. Interestingly, homopolymeric {polyguanine [poly(G)]} tracts were detected at the 5′ ends within the open reading frames. By flow cytometry, using human IgD and fluorescein isothiocyanate-conjugated anti-IgD polyclonal antibodies, most strains showed two peaks: one high- and one low-intensity peak. All isolates expressing high levels of MID had 1, 2, or 3 triplets of G's in their poly(G) tracts, while strains not expressing MID had 4, 7, 8, or 10 G’s in their poly(G) tracts or point mutations causing a putative preterminated translation. Northern blot analysis revealed that themidgene was regulated at the transcriptional level. Experiments with nonclumping variants ofM.catarrhalisproved that bacteria lost their MID expression by removing a G in their poly(G) tracts.Moraxellastrains isolated from the nasopharynx or from blood and sputum specimens expressed MID at approximately the same frequency. In addition, no variation was observed between strains of different geographical origins (Australia, Europe, Japan, or the United States). MID and themidgene were found solely inM.catarrhalis, whereas relatedNeisseriaandMoraxellaspecies did not express MID. Taken together, MID appears to be a conserved protein that can be found in essentially allM.catarrhalisstrains. Furthermore, MID is governed by poly(G) tracts when bacteria undergo phase variation.
Evidence for Horizontal Transfer of the
Eco
T38I Restriction- Modification Gene to Chromosomal DNA by the P2 Phage and Diversity of Defective P2 Prophages in
Escherichia
coli
TH38 Strains
Authors: Kita Keiko , Kawakami Hideaki , Tanaka Hiroaki 
Published: March 2003

ABSTRACT

A DNA fragment carrying the genes coding for a novel
Eco
T38I restriction endonuclease (R.
Eco
T38I) and
Eco
T38I methyltransferase (M.
Eco
T38I), which recognize G(A/G)GC(C/T)C, was cloned from the chromosomal DNA of
Escherichia
coli
TH38. The endonuclease and methyltransferase genes were in a head-to-head orientation and were separated by a 330-nucleotide intergenic region. A third gene, the C.
Eco
T38I gene, was found in the intergenic region, partially overlapping the R.
Eco
T38I gene. The gene product, C.
Eco
T38I, acted as both a positive regulator of R.
Eco
T38I gene expression and a negative regulator of M.
Eco
T38I gene expression. M.
Eco
T38I purified from recombinant
E
.
coli
cells was shown to be a monomeric protein and to methylate the inner cytosines in the recognition sequence. R.
Eco
T38I was purified from
E
.
coli
HB101 expressing M.
Eco
T38I and formed a homodimer. The
Eco
T38I restriction (R)-modification (M) system (R-M system) was found to be inserted between the
A
and
Q
genes of defective bacteriophage P2, which was lysogenized in the chromosome at
loc
I, one of the P2 phage attachment sites observed in both
E
.
coli
K-12 MG1655 and TH38 chromosomal DNAs. Ten strains of
E
.
coli
TH38 were examined for the presence of the
Eco
T38I R-M gene on the P2 prophage. Conventional PCR analysis and assaying of R activity demonstrated that all strains carried a single copy of the
Eco
T38I R-M gene and expressed R activity but that diversity of excision in the
ogr
,
D
,
H
,
I
, and
J
genes in the defective P2 prophage had arisen.
Heterocyst-Specific Expression of
patB
, a Gene Required for Nitrogen Fixation in
Anabaena
sp. Strain PCC 7120
Authors: Jones Kathryn M. , Buikema William J. , Haselkorn Robert 
Published: March 2003

ABSTRACT

The
patB
gene product is required for growth and survival of the filamentous cyanobacterium
Anabaena
sp. strain PCC 7120 in the absence of combined nitrogen. A
patB
::
gfp
fusion demonstrated that this gene is expressed exclusively in heterocysts.
patB
mutants have a normal initial pattern of heterocyst spacing along the filament but differentiate excess heterocysts after several days in the absence of combined nitrogen. Expression of
hetR
and
patS
, two critical regulators of the heterocyst development cascade, are normal for
patB
mutants, indicating that
patB
acts downstream of them in the differentiation pathway. A
patB
deletion mutant suffers an almost complete cessation of growth and nitrogen fixation within 24 h of combined nitrogen removal. In contrast, a new PatB mutant that is defective in its N-terminal ferredoxin domain, or a previously described mutant that has a frameshift removing its C-terminal helix-turn-helix domain, grows very slowly and differentiates multiple contiguous heterocysts under nitrogen-deficient conditions.
Identification of a New Gene Essential for GerminationofBacillus subtilisSpores withCa2+-Dipicolinate
Authors: Ragkousi Katerina , Eichenberger Patrick , van Ooij Christiaan , Setlow Peter 
Published: March 2003

ABSTRACTBacillus subtilisspores can germinate with a 1:1 chelate of Ca2+and dipicolinic acid (DPA), a compound present at high levels in the spore core. Using a genetic screen to identify genes encoding proteins that are specifically involved in spore germination by Ca2+-DPA, three mutations were identified. One was in the gene encoding the cortex lytic enzyme, CwlJ, that was previously shown to be essential for spore germination by Ca2+-DPA. The other two were mapped to an open reading frame,ywdL, encoding a protein of unknown function. Analysis ofywdLexpression showed that the gene is expressed during sporulation in the mother cell compartment of the sporulating cell and that its transcription is σEdependent. Functional characterization of YwdL demonstrated that it is a new spore coat protein that is essential for the presence of CwlJ in the spore coat. Assembly of YwdL itself into the spore coat is dependent on the coat morphogenetic proteins CotE and SpoIVA. However, other than lacking CwlJ,ywdLspores have no obvious defect in their spore coat. Because of the role for YwdL in a part of the spore germination process, we propose renamingywdLas a spore germination gene,gerQ.
Comparative Genomics of
Salmonella
enterica
Serovar Typhi Strains Ty2 and CT18
Authors: Deng Wen , Liou Shian-Ren , Plunkett Guy , Mayhew George F. , Rose Debra J. , Burland Valerie , Kodoyianni Voula , Schwartz David C. , Blattner Frederick R. 
Published: March 2003

ABSTRACT

We present the 4.8-Mb complete genome sequence of
Salmonella
enterica
serovar Typhi strain Ty2, a human-specific pathogen causing typhoid fever. A comparison with the genome sequence of recently isolated
S
.
enterica
serovar Typhi strain CT18 showed that 29 of the 4,646 predicted genes in Ty2 are unique to this strain, while 84 genes are unique to CT18. Both genomes contain more than 200 pseudogenes; 9 of these genes in CT18 are intact in Ty2, while 11 intact CT18 genes are pseudogenes in Ty2. A half-genome interreplichore inversion in Ty2 relative to CT18 was confirmed. The two strains exhibit differences in prophages, insertion sequences, and island structures. While CT18 carries two plasmids, one conferring multiple drug resistance, Ty2 has no plasmids and is sensitive to antibiotics.
TheStreptomyces coelicolorDevelopmental Transcription Factor σBldNIs Synthesized as a Proprotein
Authors: Bibb Maureen J. , Buttner Mark J. 
Published: March 2003

ABSTRACTbldNis one of a set of genes required for the formation of specialized, spore-bearing aerial hyphae during differentiation in the mycelial bacteriumStreptomyces coelicolor. Previous analysis (M. J. Bibb et al., J. Bacteriol. 182:4606-4616, 2000) showed thatbldNencodes a member of the extracytoplasmic function subfamily of RNA polymerase σ factors and that translation from the most strongly predicted start codon (GTG1) would give rise to a σ factor having an unusual N-terminal extension of ca. 86 residues. Here, by using a combination of site-directed mutagenesis and immunoblot analysis, we provide evidence that allbldNtranslation arises from initiation at GTG1and that the primary translation product is a proprotein (pro-σBldN) that is proteolytically processed to a mature species (σBldN) by removal of most of the unusual N-terminal extension. A time course taken during differentiation of the wild type on solid medium showed early production of pro-σBldNand the subsequent appearance of mature σBldN, which was concomitant with aerial mycelium formation and the disappearance of pro-σBldN. Two genes encoding members of a family of metalloproteases that are involved in the regulated proteolytic processing of transcription factors in other organisms were identified in theS. coelicolorgenome, but their disruption did not affect differentiation or pro-σBldNprocessing.
Localization of rRNA Synthesis inBacillus subtilis: Characterization of Loci Involved in Transcription Focus Formation
Authors: Davies Karen M. , Lewis Peter J. 
Published: March 2003

ABSTRACTInBacillus subtilis, RNA polymerase becomes concentrated into regions of the nucleoid called transcription foci. With green fluorescent protein-tagged RNA polymerase, these structures are only observed at higher growth rates and have been shown to represent the sites of rRNA synthesis. There are 10 rRNA (rrn) operons distributed around nearly half of the chromosome. In this study we analyzed therrncomposition of transcription foci with fluorescently tagged loci and showed that they comprise the origin-proximal operonrrnObut not the more dispersedrrnEorrrnD. This suggests that transcription foci comprise only the seven origin-proximal operonsrrnO,rrnA,rrnJ,rrnW,rrnI,rrnH, andrrnG. These results have important implications for our understanding of microbial chromosome structure.
CheZ Phosphatase Localizes to Chemoreceptor Patches via CheA-Short
Authors: Cantwell Brian J. , Draheim Roger R. , Weart Richard B. , Nguyen Cameran , Stewart Richard C. , Manson Michael D. 
Published: March 2003

ABSTRACT

We have investigated the conditions required for polar localization of the CheZ phosphatase by using a CheZ-green fluorescent protein fusion protein that, when expressed from a single gene in the chromosome, restored chemotaxis to a Δ
cheZ
strain. Localization was observed in wild-type, Δ
cheZ
, Δ
cheYZ
, and Δ
cheRB
cells but not in cells with
cheA
,
cheW
, or all chemoreceptor genes except
aer
deleted. Cells making only CheA-short (CheA
S
) or CheA lacking the P2 domain also retained normal localization, whereas cells producing only CheA-long or CheA missing the P1 and P2 domains did not. We conclude that CheZ localization requires the truncated C-terminal portion of the P1 domain present in CheA
S
. Missense mutations targeting residues 83 through 120 of CheZ also abolished localization. Two of these mutations do not disrupt chemotaxis, indicating that they specifically prevent interaction with CheA
S
while leaving other activities of CheZ intact.
Genome Organization and Molecular Analysis of the Temperate Bacteriophage MM1 of
Streptococcus pneumoniae
Authors: Obregón Virginia , García José L. , García Ernesto , López Rubens , García Pedro 
Published: March 2003

ABSTRACT

The genome of MM1 (40,248 bp), a temperate bacteriophage from the Spain
23F
-1 multiresistant epidemic clone of
Streptococcus pneumoniae
, is organized in 53 open reading frames (ORFs) and in at least five functional clusters. Bioinformatic and N-terminal amino acid sequence analyses enabled the assignment of possible functions to 26 ORFs. Analyses comparing the MM1 genome with those of other bacteriophages revealed similarities, mainly with genomes of phages infecting gram-positive bacteria, which suggest recent exchange of genes between species colonizing the same habitat.
Structural and Functional Analysis of a Putative Gene Cluster for Palatinose Transport on the Linear Chromosome of
Agrobacterium tumefaciens
MAFF301001
Authors: De Costa Devika M. , Suzuki Katsunori , Yoshida Kazuo 
Published: March 2003

ABSTRACT

We identified a putative
pal
gene cluster (
palR
,
palE
,
palF
,
palG
,
palK
,
palA
, and
palB
) in the plant-tumorigenic bacterium
Agrobacterium tumefaciens
MAFF301001; by sequencing analyses, this cluster was found to be involved in palatinose transport, and its functional importance was revealed by mutational analyses. The
pal
gene products were highly homologous to those of putative trehalose/maltose ABC-type transport systems but were not essential to bacterial growth on trehalose. Insertion mutations in the
palK
and
palE
genes showed the necessity of these genes for bacterial growth and chemotaxis with palatinose as the carbon source, but no inhibition of tumorigenesis was observed. Growth on trehalose and maltose was not influenced by the mutations.