bluuebunny/crossref_metadata_2025_split huggingface dataset:
TtgV Bound to a Complex Operator Site Represses Transcription of the Promoter for the Multidrug and Solvent Extrusion TtgGHI Pump
Authors: Guazzaroni María-Eugenia , Terán Wilson , Zhang Xiaodong , Gallegos María-Trinidad , Ramos Juan L. 
Published: May 2004

ABSTRACT

The TtgGHI efflux pump of
Pseudomonas putida
extrudes a variety of antibiotics and solvents. We show that the
ttgGHI
operon is transcribed in vitro and in vivo from a single promoter and not from two overlapping promoters as previously proposed. The expression of this promoter is controlled by the TtgV repressor, whose operator expands through four helical turns that overlap the −10 region of the promoter. We also show that TtgV is released from its operator on binding of effectors such as aliphatic alcohols. Mutational analysis of the
ttgGHI
promoter revealed that substitutions at −13, −12, and −8 yielded promoters that were unable to drive transcription whereas certain mutations at −9, −11, and −6 to −3 increased expression in vivo. The cause of the increased expression was either a decrease in the affinity of the TtgV protein for its operator or an increase in the affinity of RNA polymerase for the mutant promoters.
Mutations in
Haemophilus influenzae
Mismatch Repair Genes Increase Mutation Rates of Dinucleotide Repeat Tracts but Not Dinucleotide Repeat-Driven Pilin Phase Variation Rates
Authors: Bayliss Christopher D. , Sweetman Wendy A. , Moxon E. Richard 
Published: May 2004

ABSTRACT

High-frequency, reversible switches in expression of surface antigens, referred to as phase variation (PV), are characteristic of
Haemophilus influenzae
. PV enables this bacterial species, an obligate commensal and pathogen of the human upper respiratory tract, to adapt to changes in the host environment. Phase-variable hemagglutinating pili are expressed by many
H. influenzae
isolates. PV involves alterations in the number of 5′ TA repeats located between the −10 and −35 promoter elements of the overlapping, divergently orientated promoters of
hifA
and
hifBCDE
, whose products mediate biosynthesis and assembly of pili. Dinucleotide repeat tracts are destabilized by mismatch repair (MMR) mutations in
Escherichia coli
. The influence of mutations in MMR genes of
H. influenzae
strain Rd on dinucleotide repeat-mediated PV rates was investigated by using reporter constructs containing 20 5′ AT repeats. Mutations in
mutS
,
mutL
, and
mutH
elevated rates approximately 30-fold, while rates in
dam
and
uvrD
mutants were increased 14- and 3-fold, respectively. PV rates of constructs containing 10 to 12 5′ AT repeats were significantly elevated in
mutS
mutants of
H. influenzae
strains Rd and Eagan. An intact
hif
locus was found in 14 and 12% of representative nontypeable
H. influenzae
isolates associated with either otitis media or carriage, respectively. Nine or more tandem 5′ TA repeats were present in the promoter region. Surprisingly, inactivation of
mutS
in two serotype b
H. influenzae
strains did not alter pilin PV rates. Thus, although functionally analogous to the
E. coli
MMR pathway and active on dinucleotide repeat tracts, defects in
H. influenzae
MMR do not affect 5′ TA-mediated pilin PV.
Positive Control of Swarming, Rhamnolipid Synthesis, and Lipase Production by the Posttranscriptional RsmA/RsmZ System inPseudomonas aeruginosaPAO1
Authors: Heurlier Karin , Williams Faye , Heeb Stephan , Dormond Corinne , Pessi Gabriella , Singer Dustin , Cámara Miguel , Williams Paul , Haas Dieter 
Published: May 2004

ABSTRACTInPseudomonas aeruginosa, the small RNA-binding, regulatory protein RsmA is a negative control element in the formation of several extracellular products (e.g., pyocyanin, hydrogen cyanide, PA-IL lectin) as well as in the production ofN-acylhomoserine lactone quorum-sensing signal molecules. RsmA was found to control positively the ability to swarm and to produce extracellular rhamnolipids and lipase, i.e., functions contributing to niche colonization byP. aeruginosa. AnrsmAnull mutant was entirely devoid of swarming but produced detectable amounts of rhamnolipids, suggesting that factors in addition to rhamnolipids influence the swarming ability ofP. aeruginosa. A small regulatory RNA,rsmZ, which antagonized the effects of RsmA, was identified inP. aeruginosa. Expression of thersmZgene was dependent on both the global regulator GacA and RsmA, increased with cell density, and was subject to negative autoregulation. Overexpression ofrsmZand a null mutation inrsmAresulted in quantitatively similar, negative or positive effects on target genes, in agreement with a model that postulates titration of RsmA protein by RsmZ RNA.
Dual Control ofHelicobacter pyloriHeat Shock Gene Transcription by HspR and HrcA
Authors: Spohn Gunther , Danielli Alberto , Roncarati Davide , Delany Isabel , Rappuoli Rino , Scarlato Vincenzo 
Published: May 2004

ABSTRACTThe HspR repressor regulates transcription of thegroESL,hrcA-grpE-dnaK, andcbpA-hspR-orfoperons ofHelicobacter pylori. Here we show that two of the HspR-regulated operons, namely, thegroESLanddnaKoperons, encoding the major cellular chaperone machineries are also regulated by theH. pylorihomologue of the HrcA repressor. Similarly to thehspRmutation, deletion of thehrcAgene also leads to complete derepression of the Pgroand Phrcpromoters. The presence of both HspR and HrcA is therefore necessary for regulated transcription from these promoters. HrcA binds directly to Pgroand Phrc, likely contacting two inverted repeats with similarity to the CIRCE motif, which are present on both promoters. HrcA regulation is, however, shown to depend on binding of the HspR protein, since deletion of the HspR-binding site of the Pgropromoter leads to loss of heat inducibility of this promoter. In contrast, transcription from the Pcbppromoter is regulated solely by HspR. HspR is also shown to form oligomers in vivo through a stretch of hydrophobic repeats between amino acid positions 66 and 97. The implications of these findings for the elucidation of the networks regulating heat shock gene expression inH. pyloriare discussed.
Effects of a
gerF
(
lgt
) Mutation on the Germination of Spores of
Bacillus subtilis
Authors: Igarashi Takao , Setlow Barbara , Paidhungat Madan , Setlow Peter 
Published: May 2004

ABSTRACT

One of the proteins of the membrane-bound receptors that recognize individual nutrients that trigger germination of spores of
Bacillus subtilis
contains the recognition sequence for diacylglycerol addition to a cysteine residue near the protein's N terminus.
B. subtilis
spores lacking the
gerF
(
lgt
) gene that codes for prelipoprotein diacylglycerol transferase exhibited significantly slowed germination in response to nutrient germinants as found previously, but germination of
gerF
spores with a mixture of Ca
2+
and dipicolinic acid or with dodecylamine was normal, as was the spontaneous germination of
gerF
spores lacking all nutrient germinant receptors. The deleterious effects of the
gerF
mutation on nutrient germination were highest on germination triggered by the GerA nutrient receptor and were less so (but still significant) on germination triggered by the GerB nutrient receptor. However, there was little, if any, effect on GerK nutrient receptor-mediated spore germination. As predicted from the latter results, replacement by alanine of the cysteine residue to which diacylglycerol is thought to be added to these nutrient receptors had a large effect on GerA receptor function, less effect on GerB receptor function, and little, if any, effect on GerK receptor function.
Drastic Differences in Crh and HPr Synthesis Levels Reflect Their Different Impacts on Catabolite Repression in
Bacillus subtilis
Authors: Görke Boris , Fraysse Laetitia , Galinier Anne 
Published: May 2004

ABSTRACT

In
Bacillus subtilis
, carbon catabolite repression (CCR) of catabolic genes is mediated by ATP-dependent phosphorylation of HPr and Crh. Here we show that the different efficiencies with which these two proteins contribute to CCR may be due to the drastic differences in their synthesis rates under conditions that cause CCR.
PhaQ, a New Class of Poly-β-Hydroxybutyrate (PHB)-Responsive Repressor, Regulates
phaQ
and
phaP
(Phasin) Expression in
Bacillus megaterium
through Interaction with PHB
Authors: Lee Tian-Ren , Lin Jer-Sheng , Wang Shih-Shin , Shaw Gwo-Chyuan 
Published: May 2004

ABSTRACT

Bacillus megaterium
can produce poly-β-hydroxybutyrate (PHB) as carbon and energy storage materials. We now report that the
phaQ
gene, which is located upstream of the phasin-encoding
phaP
gene, codes for a new class of transcriptional regulator that negatively controls expression of both
phaQ
and
phaP
. A PhaQ binding site that plays a role in this control has been identified by gel mobility shift assays and DNase I footprinting analysis. We have also provided evidence that PhaQ could sense the presence of PHB in vivo and that artificial PHB granules could inhibit the formation of PhaQ-DNA complex in vitro by binding to PhaQ directly. These suggest that PhaQ is a PHB-responsive repressor.
Agrobacterium rhizogenes
GALLS Protein Substitutes for
Agrobacterium tumefaciens
Single-Stranded DNA-Binding Protein VirE2
Authors: Hodges Larry D. , Cuperus Josh , Ream Walt 
Published: May 2004

ABSTRACT

Agrobacterium tumefaciens
and
Agrobacterium rhizogenes
transfer plasmid-encoded genes and virulence (Vir) proteins into plant cells. The transferred DNA (T-DNA) is stably inherited and expressed in plant cells, causing crown gall or hairy root disease. DNA transfer from
A. tumefaciens
into plant cells resembles plasmid conjugation; single-stranded DNA (ssDNA) is exported from the bacteria via a type IV secretion system comprised of VirB1 through VirB11 and VirD4. Bacteria also secrete certain Vir proteins into plant cells via this pore. One of these, VirE2, is an ssDNA-binding protein crucial for efficient T-DNA transfer and integration. VirE2 binds incoming ssT-DNA and helps target it into the nucleus. Some strains of
A. rhizogenes
lack VirE2, but they still transfer T-DNA efficiently. We isolated a novel gene from
A. rhizogenes
that restored pathogenicity to
virE2
mutant
A. tumefaciens
. The GALLS gene was essential for pathogenicity of
A. rhizogenes
. Unlike VirE2, GALLS contains a nucleoside triphosphate binding motif similar to one in TraA, a strand transferase conjugation protein. Despite their lack of similarity, GALLS substituted for VirE2.
Two Separate Quorum-Sensing Systems Upregulate Transcription of the Same ABC Transporter inStreptococcus pneumoniae
Authors: Knutsen Eivind , Ween Ola , Håvarstein Leiv Sigve 
Published: May 2004

ABSTRACTStreptococcus pneumoniaesecretes two different peptide pheromones used for intercellular communication. These peptides, which have completely unrelated primary structures, activate two separate signal transduction pathways, ComABCDE and BlpABCSRH, which regulate natural genetic transformation and bacteriocin production, respectively. Each signal transduction pathway contains a response regulator (ComE and BlpR, respectively) that activates transcription of target genes by binding to similar, but not identical, imperfect direct repeat motifs. In general the direct repeat binding sites are specific for one or the other of the two response regulators, ensuring that competence development and bacteriocin production are regulated separately. However, in the present study we show that the rate of transcription of an operon, encoding an ABC transporter of unknown function, can be stimulated by both peptide pheromones. We also show that this cross-induction is due to a hybrid direct repeat motif that can respond to both ComE and BlpR. To our knowledge this kind of convergent gene regulation by two separate two-component regulatory systems has not been described before in bacteria.
Precise Excision of the Large Pathogenicity Island, SPI7, inSalmonella entericaSerovar Typhi
Authors: Bueno Susan M. , Santiviago Carlos A. , Murillo Alejandro A. , Fuentes Juan A. , Trombert A. Nicole , Rodas Paula I. , Youderian Philip , Mora Guido C. 
Published: May 2004

ABSTRACTThe large pathogenicity island (SPI7) ofSalmonella entericaserovar Typhi is a 133,477-bp segment of DNA flanked by two 52-bp direct repeats overlapping thepheU(phenylalanyl-tRNA) gene, contains 151 potential open reading frames, and includes theviaBoperon involved in the synthesis of Vi antigen. Some clinical isolates ofS. entericaserovar Typhi are missing the entire SPI7, due to its precise excision; these strains have lost the ability to produce Vi antigen, are resistant to phage Vi-II, and invade a human epithelial cell line more rapidly. Excision of SPI7 occurs spontaneously in a clinical isolate ofS. entericaserovar Typhi when it is grown in the laboratory, leaves an intact copy of thepheUgene at its novel join point, and results in the same three phenotypic consequences. SPI7 is an unstable genetic element, probably an intermediate in the pathway of lateral transfer of such pathogenicity islands among enteric gram-negative bacteria.
Nitrite-Responsive Activation of the Nitrate Assimilation Operon in Cyanobacteria Plays an Essential Role in Up-Regulation of Nitrate Assimilation Activities under Nitrate-Limited Growth Conditions
Authors: Aichi Makiko , Maeda Shin-Ichi , Ichikawa Kazuhiro , Omata Tatsuo 
Published: May 2004

ABSTRACT

NtcB of the cyanobacterium
Synechococcus elongatus
strain PCC 7942 is a LysR family protein that enhances expression of the nitrate assimilation operon (
nirA
operon) in response to the presence of nitrite, an intermediate of assimilatory nitrate reduction. Inactivation of
ntcB
in this cyanobacterium specifically abolishes the nitrite responsiveness of
nirA
operon expression, but under nitrate-replete conditions (wherein negative feedback by intracellularly generated ammonium prevails over the positive effect of nitrite) activity levels of the nitrate assimilation enzymes are marginally higher in the wild-type cells than in the mutant cells, raising the issue of whether the nitrite-promoted regulation has physiological importance. On the other hand, the strains carrying
ntcB
expressed much higher nitrate assimilation enzyme activities under nitrate-limited growth conditions than under nitrate-replete conditions whereas the
ntcB
-deficient strains showed levels of the enzyme activities lower than those seen under the nitrate-replete conditions. Although the
ntcB
mutant maintained a constant cell population in a nitrate-limited chemostat when grown as a single culture, it was diluted at a rate expected for nondividing cells when mixed with the wild-type cells and subjected to nitrate limitation in the chemostat culture system. These results demonstrated that the nitrite-promoted activation of the nitrate assimilation operon is essential for up-regulation of the nitrate assimilation activities under the conditions of nitrate limitation and for competitive utilization of nitrate.
Horizontal Transfer of CS1 Pilin Genes of EnterotoxigenicEscherichia coli
Authors: Froehlich Barbara , Holtzapple Erik , Read Timothy D. , Scott June R. 
Published: May 2004

ABSTRACTCS1 is one of a limited number of serologically distinct pili found in enterotoxigenicEscherichia coli(ETEC) strains associated with disease in people. The genes for the CS1 pilus are on a large plasmid, pCoo. We show that pCoo is not self-transmissible, although our sequence determination for part of pCoo shows regions almost identical to those in the conjugative drug resistance plasmid R64. When we introduced R64 into a strain containing pCoo, we found that pCoo was transferred to a recipient strain in mating. Most of the transconjugant pCoo plasmids result from recombination with R64, leading to acquisition of functional copies of all of the R64 transfer genes. Temporary coresidence of the drug resistance plasmid R64 with pCoo leads to a permanent change in pCoo so that it is now self-transmissible. We conclude that when R64-like plasmids are transmitted to an ETEC strain containing pCoo, their recombination may allow for spread of the pCoo plasmid to other enteric bacteria.
ClgR, a Novel Regulator of
clp
and
lon
Expression in
Streptomyces
Authors: Bellier Audrey , Mazodier Philippe 
Published: May 2004

ABSTRACT

The
clp
genes encoding the Clp proteolytic complex are widespread among living organisms. Five
clpP
genes are present in
Streptomyces.
Among them, the
clpP1 clpP2
operon has been shown to be involved in the
Streptomyces
growth cycle, as a mutation blocked differentiation at the substrate mycelium step. Four Clp ATPases have been identified in
Streptomyces coelicolor
(ClpX and three ClpC proteins) which are potential partners of ClpP1 ClpP2. The
clpC1
gene appears to be essential, since no mutant has yet been obtained.
clpP1 clpP2
and
clpC1
are important for
Streptomyces
growth, and a study of their regulation is reported here. The
clpP3 clpP4
operon, which has been studied in
Streptomyces lividans
, is induced in a
clpP1
mutant strain, and regulation of its expression is mediated via PopR, a transcriptional regulator. We report here studies of
clgR
, a paralogue of
popR
, in
S. lividans.
Gel mobility shift assays and DNase I footprinting indicate that ClgR binds not only to the
clpP1
and
clpC1
promoters, but also to the promoter of the Lon ATP-dependent protease gene and the
clgR
promoter itself. ClgR recognizes the motif GTTCGC-5N-GCG. In vivo, ClgR acts as an activator of
clpC1
gene and
clpP1
operon expression. Similarly to PopR, ClgR degradation might be ClpP dependent and could be mediated via recognition of the two carboxy-terminal alanine residues.
Contribution of the RpoA C-Terminal Domain to Stimulation of the
Salmonella enterica hilA
Promoter by HilC and HilD
Authors: Olekhnovich Igor N. , Kadner Robert J. 
Published: May 2004

ABSTRACT

Expression of invasion genes in
Salmonella
pathogenicity island 1 (SPI-1) is mainly driven by the transcriptional activator HilA. Transcription of
hilA
is subject to complex control and is stimulated by the SPI-1-encoded HilC and HilD proteins. The C-terminal domain of RpoA contributes to
hilA
activation by HilC/D under certain inducing conditions.
Lipid II-Mediated Pore Formation by the Peptide Antibiotic Nisin: a Black Lipid Membrane Study
Authors: Wiedemann Imke , Benz Roland , Sahl Hans-Georg 
Published: May 2004

ABSTRACT
The antibiotic peptide nisin is the first known lantibiotic that uses a docking molecule within the bacterial cytoplasmic membrane for pore formation. Through specific interaction with the cell wall precursor lipid II, nisin forms defined pores which are stable for seconds and have pore diameters of 2 to 2.5 nm.
The Nucleotide Transporter of
Caedibacter caryophilus
Exhibits an Extended Substrate Spectrum Compared to the Analogous ATP/ADP Translocase of
Rickettsia prowazekii
Authors: Daugherty Robin M. , Linka Nicole , Audia Jonathon P. , Urbany Claude , Neuhaus H. Ekkehard , Winkler Herbert H. 
Published: May 2004

ABSTRACT

The two obligate intracellular alphaproteobacteria
Rickettsia prowazekii
and
Caedibacter caryophilus
, a human pathogen and a paramecium endosymbiont, respectively, possess transport systems to facilitate ATP uptake from the host cell cytosol. These transport proteins, which have 65% identity at the amino acid level, were heterologously expressed in
Escherichia coli
, and their properties were compared. The results presented here demonstrate that the caedibacter transporter had a broader substrate than the more selective rickettsial transporter. ATP analogs with modified sugar moieties, dATP and ddATP, inhibited the transport of ATP by the caedibacter transporter but not by the rickettsial transporter. Both transporters were specific for di- and trinucleotides with an adenine base in that adenosine tetraphosphate, AMP, UTP, CTP, and GTP were not competitive inhibitors. Furthermore, the antiporter nature of both transport systems was shown by the dependence of the efflux of [α-
32
P]ATP on the influx of substrate (ATP but not dATP for rickettsiae, ATP or dATP for caedibacter).
Characterization of a Nucleotide-Binding Domain Associated with Neisserial Iron Transport
Authors: Lau Gloria H. Y. , MacGillivray Ross T. A. , Murphy Michael E. P. 
Published: May 2004

ABSTRACT

The
fbpABC
operon in
Neisseria gonorrhoeae
encodes an ATP-binding cassette transporter required for iron uptake from the host ferric binding proteins. The gene for the nucleotide-binding domain (
fbpC
) expressed in
Escherichia coli
has intrinsic ATPase activity (0.5 mmol/min/mg) uncoupled from the iron transport process. The FbpC E164D mutant is found to have a 10-fold reduction in specific activity. FbpC is covalently modified by 8-azido-[γ
32
P]ATP, indicating that FbpC is a functional ATPase that likely combines with FbpB to form a ferric iron transporter.
A Phage Protein Confers Resistance to the Lactococcal Abortive Infection Mechanism AbiP
Authors: Domingues Susana , Chopin Alain , Ehrlich S. Dusko , Chopin Marie-Christine 
Published: May 2004

ABSTRACT

Phage bIL66M1 is sensitive to the lactococcal abortive infection mechanism AbiP. No spontaneous AbiP-resistant variant could be obtained at a frequency of <10
−10
. However, AbiP-resistant variants were readily obtained during infection with both bIL66M1 and the highly homologous AbiP-resistant phage bIL170. Gain of AbiP resistance was due to the acquisition of the
e6
gene from bIL170.
LFA-1 signaling through p44/42 is coupled to perforin degranulation in CD56+CD8+ natural killer cells
Authors: Perez Omar D. , Mitchell Dennis , Jager Gina C. , Nolan Garry P. 
Published: May 2004

AbstractLeukocyte function antigen 1 (LFA-1) is essential for the formation of immune cell synapses and plays a role in the pathophysiology of various autoimmune diseases. We investigated the molecular details of LFA-1 activation during adhesion between cytotoxic cells and a target model leukemia cell. The cytolytic activity of a CD3–CD8+CD56+ natural killer (NK) subset was enhanced when LFA-1 was activated. In a comparison of LFA-1 ligands, intercellular adhesion molecule 2 (ICAM-2) and ICAM-3 promoted LFA-1–directed perforin release, whereas ICAM-1 had little effect. Ligand-induced LFA-1 clustering facilitated perforin release, demonstrating LFA-1 could regulate degranulation mechanisms. LFA-1 induced the activation of src family kinases, Vav1 and p44/42 mitogen-activated protein kinase (MAPK), in human CD56+ NK cells as evidenced by intracellular phospho-epitope measurements that correlated with effector-target cell binding and perforin-granzyme A–mediated cytolytic activity. These results identify novel, specific functional consequence of LFA-1–mediated cytolytic activity in perforin-containing human NK subsets.