bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PDZ Domain of the SpoIVB Serine Peptidase Facilitates Multiple Functions
Authors: Hoa Ngo T. , Brannigan James A. , Cutting Simon M. 
Published: July 2002

ABSTRACT

During spore formation in
Bacillus subtilis
, the SpoIVB protein is a critical component of the ς
K
regulatory checkpoint. SpoIVB has been shown to be a serine peptidase that is synthesized in the spore chamber and which self-cleaves, releasing active forms. These forms can signal proteolytic processing of the transcription factor ς
K
in the outer mother cell chamber of the sporulating cell. This forms the basis of the ς
K
checkpoint and ensures accurate ς
K
-controlled gene expression. SpoIVB has also been shown to activate a second distinct process, termed the second function, which is essential for the formation of heat-resistant spores. In addition to the serine peptidase domain, SpoIVB contains a PDZ domain. We have altered a number of conserved residues in the PDZ domain by site-directed mutagenesis and assayed the sporulation phenotype and signaling properties of mutant SpoIVB proteins. Our work has revealed that the SpoIVB PDZ domain could be used for up to four distinct processes, (i) targeting of itself for
trans
proteolysis, (ii) binding to the protease inhibitor BofC, (iii) signaling of pro-ς
K
processing, and (iv) signaling of the second function of SpoIVB.
Iron-Dependent Transcription of the
frpB
Gene of
Helicobacter pylori
Is Controlled by the Fur Repressor Protein
Authors: Delany Isabel , Pacheco Ana Beatriz F. , Spohn Gunther , Rappuoli Rino , Scarlato Vincenzo 
Published: July 2002

ABSTRACT

We have overexpressed and purified the
Helicobacter pylori
Fur protein and analyzed its interaction with the intergenic regions of divergent genes involved in iron uptake (
frpB
and
ceuE
) and oxygen radical detoxification (
katA
and
tsaA
). DNase I footprint analysis showed that Fur binds specifically to a high-affinity site overlapping the
P

frpB

promoter and to low-affinity sites located upstream from promoters within both the
frpB-katA
and
ceuE-tsaA
intergenic regions. Construction of an isogenic
fur
mutant indicated that Fur regulates transcription from the P

frpB

promoter in response to iron. In contrast, no effect by either Fur or iron was observed for the other promoters.
Identification and Characterization of Tn
4656
, a Novel Class II Transposon Carrying a Set of Toluene-Degrading Genes from TOL Plasmid pWW53
Authors: Tsuda Masataka , Genka Hiroyuki 
Published: July 2002

ABSTRACT

It has been reported that the toluene-degrading (
xyl
) genes from
Pseudomonas putida
plasmid pWW53 are able to translocate to broad-host-range drug resistance plasmid RP4, and pWW53-4 is one of the smallest RP4 derivatives (H. Keil, S. Keil, R. W. Pickup, and P. A. Williams, J. Bacteriol. 164:887–895, 1985). Our investigation of pWW53-4 in this study demonstrated that such a translocated region that is 39 kb long is a transposon. This mobile element, Tn
4656
, was classified as a class II transposon since its transposition occurred by a two-step process: transposase (TnpA)-mediated formation of the cointegrate and resolvase (TnpR)-mediated site-specific resolution of the cointegrate at the two copies of the
res
site. The Tn
4656
TnpA and TnpR functions encoded in the rightmost 4-kb region were found to be exchangeable with those specified by other Tn
1721
-related class II transposons, including another toluene transposon, Tn
4653
. Sequence analysis of the transposition-related genes and sites of Tn
4656
also supported the hypothesis that this transposon is closely related to the Tn
1721
-related transposons. The lower transposition frequency of Tn
4656
has been suggested to be due to the unique nucleotide sequence of one of the terminal 39-bp inverted repeats.
In Vivo Effects of Sporulation Kinases on Mutant Spo0A Proteins in
Bacillus subtilis
Authors: Quisel John D. , Burkholder William F. , Grossman Alan D. 
Published: July 2002

ABSTRACT

The phosphorylated form of the response regulator Spo0A (Spo0A∼P) is required for the initiation of sporulation in
Bacillus subtilis
. Phosphate is transferred to Spo0A from at least four histidine kinases (KinA, KinB, KinC, and KinD) by a phosphotransfer pathway composed of Spo0F and Spo0B. Several mutations in
spo0A
allow initiation of sporulation in the absence of
spo0F
and
spo0B
, but the mechanisms by which these mutations allow bypass of
spo0F
and
spo0B
are not fully understood. We measured the ability of KinA, KinB, and KinC to activate sporulation of five
spo0A
mutants in the absence of Spo0F and Spo0B. We also determined the effect of Spo0E, a Spo0A∼P-specific phosphatase, on sporulation of strains containing the
spo0A
mutations. Our results indicate that several of the mutations relax the specificity of Spo0A, allowing Spo0A to obtain phosphate from a broader group of phosphodonors. In the course of these experiments, we observed medium-dependent effects on the sporulation of different mutants. This led us to identify a small molecule, acetoin, that can stimulate sporulation of some
spo0A
mutants.
Multiple Regulatory Mechanisms Act on the 5′ Untranslated Region of the S-Layer Gene from
Thermus thermophilus
HB8
Authors: Castán Pablo , de Pedro Miguel A. , Risco Cristina , Vallés Cristina , Fernández Luis A. , Schwarz Heinz , Berenguer José 
Published: July 2002

ABSTRACT

The role of the 5′ untranslated region (5′UTR) of the S-layer gene from
Thermus thermophilus
was analyzed through the isolation of Δ5′UTR mutants. In these mutants the half-life of
splA
mRNA was strongly reduced and
slpA
transcription was no longer subjected to growth phase-dependent repression. Overproduction and detachment of the external envelopes of the mutants were observed in stationary phase.
S-Layer Variation in
Bacillus stearothermophilus
PV72 Is Based on DNA Rearrangements between the Chromosome and the Naturally Occurring Megaplasmids
Authors: Scholz Holger C. , Riedmann Eva , Witte Angela , Lubitz Werner , Kuen Beatrix 
Published: July 2002

ABSTRACT

Bacillus stearothermophilus
PV72 expresses different S-layer genes (
sbsA
and
sbsB
) under different growth conditions. No stretches of significant sequence identity between
sbsA
and
sbsB
were detected. In order to investigate S-layer gene regulation in
B. stearothermophilus
PV72, we characterized the upstream regulatory region of
sbsA
and
sbsB
by sequencing and primer extension analysis. Both genes are transcribed from unique but different promoters, independently of the growth phase. Localization of
sbsB
in the
sbsA
-expressing strain PV72/p6 revealed that the coding region of the second S-layer gene
sbsB
is located not on the chromosome but on a natural megaplasmid of the strain, whereas the upstream regulatory region of
sbsB
was exclusively detected on the chromosome of PV72/p6. For
sbsB
expression, the coding region has to be integrated into the chromosomally located expression site. After the switch to
sbsB
expression, the
sbsA
coding region was removed from the chromosome but could still be detected on the plasmid of the
sbsB
-expressing strain PV72/p2. The
sbsA
upstream regulatory region, however, remained on the chromosome. This is the first report of S-layer variation not caused by intrachromosomal DNA rearrangements, but where variant formation depends on recombinational events between the plasmid and the chromosome.
Anaerobic Initial Reaction of
n
-Alkanes in a Denitrifying Bacterium: Evidence for (1-Methylpentyl)succinate as Initial Product and for Involvement of an Organic Radical in
n
-Hexane Metabolism
Authors: Rabus Ralf , Wilkes Heinz , Behrends Astrid , Armstroff Antje , Fischer Thomas , Pierik Antonio J. , Widdel Friedrich 
Published: July 2002

ABSTRACT

A novel type of denitrifying bacterium (strain HxN1) with the capacity to oxidize
n
-alkanes anaerobically with nitrate as the electron acceptor to CO
2
formed (1-methylpentyl)succinate (MPS) during growth on
n
-hexane as the only organic substrate under strict exclusion of air. Identification of MPS by gas chromatography-mass spectrometry was based on comparison with a synthetic standard. MPS was not formed during anaerobic growth on
n
-hexanoate. Anaerobic growth with [1-
13
C]
n
-hexane or
d
14
-
n
-hexane led to a 1-methylpentyl side chain in MPS with one
13
C atom or 13 deuterium atoms, respectively. This indicates that the 1-methylpentyl side chain originates directly from
n
-hexane. Electron paramagnetic resonance spectroscopy revealed the presence of an organic radical in
n
-hexane-grown cells but not in
n
-hexanoate-grown cells. Results point at a mechanistic similarity between the anaerobic initial reaction of
n
-hexane and that of toluene, even though
n
-hexane is much less reactive; the described initial reaction of toluene in anaerobic bacteria is an addition to fumarate via a radical mechanism yielding benzylsuccinate. We conclude that
n
-hexane is activated at its second carbon atom by a radical reaction and presumably added to fumarate as a cosubstrate, yielding MPS as the first stable product. When 2,3-
d
2
-fumarate was added to cultures growing on unlabeled
n
-hexane, 3-
d
1
-MPS rather than 2,3-
d
2
-MPS was detected, indicating loss of one deuterium atom by an as yet unknown mechanism.
Effects of Ribosomes and Intracellular Solutes on Activities and Stabilities of Elongation Factor 2 Proteins from Psychrotolerant and Thermophilic Methanogens
Authors: Thomas Torsten , Kumar Naresh , Cavicchioli Ricardo 
Published: July 2002

ABSTRACT

Low-temperature-adapted archaea are abundant in the environment, yet little is known about the thermal adaptation of their proteins. We have previously compared elongation factor 2 (EF-2) proteins from Antarctic (
Methanococcoides burtonii
) and thermophilic (
Methanosarcina thermophila
) methanogens and found that the
M. burtonii
EF-2 had greater intrinsic activity at low temperatures and lower thermal stability at high temperatures (T. Thomas and R. Cavicchioli, J. Bacteriol. 182:1328–1332, 2000). While the gross thermal properties correlated with growth temperature, the activity and stability profiles of the EF-2 proteins did not precisely match the optimal growth temperature of each organism. This indicated that intracellular components may affect the thermal characteristics of the EF-2 proteins, and in this study we examined the effects of ribosomes and intracellular solutes. At a high growth temperature the thermophile produced high levels of potassium glutamate, which, when assayed in vitro with EF-2, retarded thermal unfolding and increased catalytic efficiency. In contrast, for the Antarctic methanogen adaptation to growth at a low temperature did not involve the accumulation of stabilizing organic solutes but appeared to result from an increased affinity of EF-2 for GTP and high levels of EF-2 in the cell relative to its low growth rate. Furthermore, ribosomes greatly stimulated GTPase activity and moderately stabilized both EF-2 proteins. These findings illustrate the different physiological strategies that have evolved in two phylogenetically related but thermally distinct methanogens to enable EF-2 to function satisfactorily.
Phase-Variable Expression of an Operon Encoding Extracellular Alkaline Protease, a Serine Protease Homolog, and Lipase in
Pseudomonas brassicacearum
Authors: Chabeaud Philippe , de Groot Arjan , Bitter Wilbert , Tommassen Jan , Heulin Thierry , Achouak Wafa 
Published: July 2002

ABSTRACT

The rhizobacterium
Pseudomonas brassicacearum
forms phenotypic variants which do not show extracellular protease and lipase activity. The operon encoding these enzymes, a serine protease homolog, and a type I secretion machinery was characterized. Transcriptional
lacZ
gene fusions revealed that the expression of the operon is under the control of phase variation.
FosB, a Cysteine-Dependent Fosfomycin Resistance Protein under the Control of ς
W
, an Extracytoplasmic-Function ς Factor in
Bacillus subtilis
Authors: Cao Min , Bernat Bryan A. , Wang Zhepeng , Armstrong Richard N. , Helmann John D. 
Published: July 2002

ABSTRACT

We demonstrate that the
Bacillus subtilis fosB(yndN)
gene encodes a fosfomycin resistance protein. Expression of
fosB
requires ς
W
, and both
fosB
and
sigW
mutants are fosfomycin sensitive. FosB is a metallothiol transferase related to the FosA class of Mn
2+
-dependent glutathione transferases but with a preference for Mg
2+
and
l
-cysteine as cofactors.
Molecular Sieve Mechanism of Selective Release of Cytoplasmic Proteins by Osmotically Shocked
Escherichia coli
Authors: Vázquez-Laslop Nora , Lee Hyunwoo , Hu Rong , Neyfakh Alex A. 
Published: July 2002

ABSTRACT

Escherichia coli
cells, the outer membrane of which is permeabilized with EDTA, release a specific subset of cytoplasmic proteins upon a sudden drop in osmolarity in the surrounding medium. This subset includes EF-Tu, thioredoxin, and DnaK among other proteins, and comprises ∼10% of the total bacterial protein content. As we demonstrate here, the same proteins are released from electroporated
E. coli
cells pretreated with EDTA. Although known for several decades, the phenomenon of selective release of proteins has received no satisfactory explanation. Here we show that the subset of released proteins is almost identical to the subset of proteins that are able to pass through a 100-kDa-cutoff cellulose membrane upon molecular filtration of an
E. coli
homogenate. This finding indicates that in osmotically shocked or electroporated bacteria, proteins are strained through a molecular sieve formed by the transiently damaged bacterial envelope. As a result, proteins of small native sizes are selectively released, whereas large proteins and large protein complexes are retained by bacterial cells.
NreB from
Achromobacter xylosoxidans
31A Is a Nickel-Induced Transporter Conferring Nickel Resistance
Authors: Grass Gregor , Fan Bin , Rosen Barry P. , Lemke Karin , Schlegel Hans-Günter , Rensing Christopher 
Published: July 2002

ABSTRACT

There are two distinct nickel resistance loci on plasmid pTOM9 from
Achromobacter xylosoxidans
31A,
ncc
and
nre
. Expression of the
nreB
gene was specifically induced by nickel and conferred nickel resistance on both
A. xylosoxidans
31A and
Escherichia coli. E. coli
cells expressing
nreB
showed reduced accumulation of Ni
2+
, suggesting that NreB mediated nickel efflux. The histidine-rich C-terminal region of NreB was not essential but contributed to maximal Ni
2+
resistance.
WbjA Adds Glucose To Complete the O-Antigen Trisaccharide Repeating Unit of the Lipopolysaccharide of
Pseudomonas aeruginosa
Serogroup O11
Authors: Dean Charles R. , Datta Anup , Carlson Russell W. , Goldberg Joanna B. 
Published: July 2002

ABSTRACT

Lipopolysaccharide from a
wbjA
mutant, deficient in a putative glycosyltransferase from
Pseudomonas aeruginosa
serogroup O11, was compared to that from an O-antigen polymerase mutant. Results suggest that WbjA adds the terminal glucose to complete the serogroup O11 O-antigen unit and identifies the biological repeating unit as [-2)-β-D-glucose-(1-3)-α-L-
N
-acetylfucosamine-(1-3)-β-D-
N
-acetylfucosamine-(1].
The O-Antigen Gene Cluster of
Escherichia coli
O55:H7 and Identification of a New UDP-GlcNAc C4 Epimerase Gene
Authors: Wang Lei , Huskic Sandy , Cisterne Adam , Rothemund Deborah , Reeves Peter R. 
Published: July 2002

ABSTRACT

Escherichia coli
O55 is an important antigen which is often associated with enteropathogenic
E. coli
clones. We sequenced the genes responsible for its synthesis and identified genes for O-antigen polymerase, O-antigen flippase, four enzymes involved in GDP-colitose synthesis, and three glycosyltransferases, all by comparison with known genes. Upstream of the normal O-antigen region there is a
gne
gene, which encodes a UDP-GlcNAc epimerase for converting UDP-GlcNAc to UDP-GalNAc and is essential for O55 antigen synthesis. The O55
gne
product has only 20 and 26% identity to the
gne
genes of
Pseudomonas aeruginosa
and
E. coli
O113, respectively. We also found evidence for the O55 gene cluster's having evolved from another gene cluster by gain and loss of genes. Only three of the GDP-colitose pathway genes are in the usual location, the other two being separated, although nearby. It is thought that the
E. coli
O157:H7 clone evolved from the O55:H7 clone in part by transfer of the O157 gene cluster into an O55 lineage. Comparison of genes flanking the O-antigen gene clusters of the O55:H7 and O157:H7 clones revealed one recombination site within the
galF
gene and located the other between the
hisG
and
amn
genes. Genes outside the recombination sites are 99.6 to 100% identical in the two clones, while most genes thought to have transferred with the O157 gene cluster are 95 to 98% identical.
Identification and Physical Characterization of the HbpR Binding Sites of the
hbpC
and
hbpD
Promoters
Authors: Tropel David , Roelof van der Meer Jan 
Published: July 2002

ABSTRACT

Pseudomonas azelaica
HBP1 can use 2-hydroxybiphenyl (2-HBP) and 2,2′-dihydroxybiphenyl as sole carbon and energy sources by means of the
hbp
regulon. This regulon is composed of three genes,
hbpCA
and
hbpD
, coding for enzymes of a
meta
-cleavage pathway and the
hbpR
gene, which codes for a XylR/DmpR-type transcription regulator. It was previously shown that HbpR activates transcription from two σ
54
-dependent promoters, P

hbpC

and P

hbpD

, in the presence of 2-HBP. In this study, by using gel mobility shift assays with a purified fusion protein containing calmodulin binding protein (CBP) and HbpR, we detected two binding regions for HbpR in P

hbpC

and one binding region in P

hbpD

. DNase I footprints of the proximal binding region of P

hbpC

and of the binding region in P

hbpD

showed that CBP-HbpR protected a region composed of two inverted repeat sequences which were homologous to the binding sites identified for XylR. Unlike the situation in the XylR/P

u

system, we observed simultaneous binding of CBP-HbpR on the two upstream activating sequences (UASs). Fragments with only one UAS did not show an interaction with HbpR, indicating that both pairs of UASs are needed for HbpR binding. The addition of both ATP and 2-HBP increased the DNA binding affinity of HbpR. These results showed for the first time that, for regulators of the XylR/DmpR type, the effector positively affects the recruitment of the regulatory protein on the enhancer DNA.
Repression of the
Staphylococcus aureus
Accessory Gene Regulator in Serum and In Vivo
Authors: Yarwood Jeremy M. , McCormick John K. , Paustian Michael L. , Kapur Vivek , Schlievert Patrick M. 
Published: July 2002

ABSTRACT

Subgenomic DNA microarrays were employed to evaluate the expression of the accessory gene regulator (
agr
locus) as well as multiple virulence-associated genes in
Staphylococcus aureus
. Gene expression was examined during growth of
S. aureus
in vitro in standard laboratory medium and rabbit serum and in vivo in subcutaneous chambers implanted in either nonimmune rabbits or rabbits immunized with staphylococcal enterotoxin B. Expression of RNAIII, the effector molecule of the
agr
locus, was dramatically repressed in serum and in vivo, despite the increased expression of secreted virulence factors sufficient to cause toxic shock syndrome (TSS) in the animals. Statistical analysis and clustering of virulence genes based on their expression profiles in the various experimental conditions demonstrated no positive correlation between the expression of
agr
and any staphylococcal virulence factors examined. Disruption of the
agr
locus had only a minimal effect on the expression in vivo of the virulence factors examined. An effect of immunization on the expression of
agr
and virulence factors was also observed. These results suggest that
agr
activation is not necessary for development of staphylococcal TSS and that regulatory circuits responding to the in vivo environment override
agr
activity.
Induction of ResDE-Dependent Gene Expression in
Bacillus subtilis
in Response to Nitric Oxide and Nitrosative Stress
Authors: Nakano Michiko M. 
Published: July 2002

ABSTRACT

Transcription of ResDE-controlled genes in
Bacillus subtilis
was induced by sodium nitroprusside and nitric oxide. This induction requires the sensor kinase ResE and the response regulator ResD. Among members of the ResDE regulon, only the flavohemoglobin gene was induced by nitrosative stress via both a ResDE-dependent mechanism and an unidentified ResDE-independent mechanism.
Metabolic Signals That Lead to Control of
CBB
Gene Expression in
Rhodobacter capsulatus
Authors: Tichi Mary A. , Tabita F. Robert 
Published: July 2002

ABSTRACT

Various mutant strains were used to examine the regulation and metabolic control of the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway in
Rhodobacter capsulatus
. Previously, a ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO)-deficient strain (strain SBI/II) was found to show enhanced levels of
cbb
I
and
cbb
II
promoter activities during photoheterotrophic growth in the presence of dimethyl sulfoxide. With this strain as the starting point, additional mutations were made in genes encoding phosphoribulokinase and transketolase and in the gene encoding the LysR-type transcriptional activator, CbbR
II
. These strains revealed that a product generated by phosphoribulokinase was involved in control of CbbR-mediated
cbb
gene expression in SBI/II. Additionally, heterologous expression experiments indicated that
Rhodobacter sphaeroides
CbbR responded to the same metabolic signal in
R. capsulatus
SBI/II and mutant strain backgrounds.
Differential DNA Binding of Transcriptional Regulator PcaU from
Acinetobacter
sp. Strain ADP1
Authors: Popp Roland , Kohl Tobias , Patz Patricia , Trautwein Gaby , Gerischer Ulrike 
Published: July 2002

ABSTRACT

Transcriptional regulator PcaU from
Acinetobacter
sp. strain ADP1 governs expression of genes for protocatechuate degradation (
pca
genes) as a repressor or an activator depending on the levels of the inducer protocatechuate and of its own gene. PcaU is a member of the IclR protein family. Here the DNA binding properties of the purified protein are described in terms of the location of the binding sites and the affinity to these sites. Native PcaU was purified after overexpression of the
pcaU
gene in
Escherichia coli
. It is a dimer in solution. The binding site in the
pcaU-pcaI
intergenic region is located between the two divergent promoters covering 45 bp, which includes three perfect 10-bp repetitions. A PcaU binding site downstream of
pcaU
is covered by PcaU across two palindromic sequence repetitions. The affinity of PcaU for the intergenic binding sites is 50-fold higher (dissociation constant [

K
d

], 0.16 nM) than the affinity for the site downstream of
pcaU
(

K
d

, 8 nM). The binding of PcaU was tested after modifications of the intergenic binding site. Removal of any external sequence repetition still allowed for specific binding of PcaU, but the affinity was significantly reduced, suggesting an important role for all three sequence repetitions in gene expression. The involvement of DNA bending in the regulatory process is suggested by the observed strong intrinsic curvature displayed by the
pcaU-pcaI
intergenic DNA.
Isolation of the Etiologic Agent of Human Granulocytic Ehrlichiosis from the White-Footed Mouse (
Peromyscus leucopus
)
Authors: Ravyn M. Dana , Kodner Carrie B. , Carter Sarah E. , Jarnefeld Janet L. , Johnson Russell C. 
Published: July 2002

ABSTRACT

We examined white-footed mice (
Peromyscus leucopus
) from Minnesota for infection with the etiologic agent of human granulocytic ehrlichiosis (HGE). From April to September 1997, we collected
P. leucopus
from Washington County, Minnesota, an area enzootic for HGE. Blood was cultivated in HL60 cells for isolation of the HGE agent. Of 59 mice examined, only a single mouse was culture positive for the HGE agent. The 16S ribosomal DNA sequence of the isolate was determined to be identical to that of the HGE agent. The isolate was reactive with monoclonal antibodies to the 44-kDa antigen of the HGE agent and was infectious for laboratory mice.