bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrio fischeri lux
Genes Play an Important Role in Colonization and Development of the Host Light Organ
Authors: Visick Karen L. , Foster Jamie , Doino Judith , McFall-Ngai Margaret , Ruby Edward G. 
Published: July 2002

ABSTRACT

The bioluminescent bacterium
Vibrio fischeri
and juveniles of the squid
Euprymna scolopes
specifically recognize and respond to one another during the formation of a persistent colonization within the host's nascent light-emitting organ. The resulting fully developed light organ contains brightly luminescing bacteria and has undergone a bacterium-induced program of tissue differentiation, one component of which is a swelling of the epithelial cells that line the symbiont-containing crypts. While the luminescence (
lux
) genes of symbiotic
V. fischeri
have been shown to be highly induced within the crypts, the role of these genes in the initiation and persistence of the symbiosis has not been rigorously examined. We have constructed and examined three mutants (
luxA
,
luxI
, and
luxR
), defective in either luciferase enzymatic or regulatory proteins. All three are unable to induce normal luminescence levels in the host and, 2 days after initiating the association, had a three- to fourfold defect in the extent of colonization. Surprisingly, these
lux
mutants also were unable to induce swelling in the crypt epithelial cells. Complementing, in
trans
, the defect in light emission restored both normal colonization capability and induction of swelling. We hypothesize that a diminished level of oxygen consumption by a luciferase-deficient symbiotic population is responsible for the reduced fitness of
lux
mutants in the light organ crypts. This study is the first to show that the capacity for bioluminescence is critical for normal cell-cell interactions between a bacterium and its animal host and presents the first examples of
V. fischeri
genes that affect normal host tissue development.
A Family of Six Flagellin Genes Contributes to the
Caulobacter crescentus
Flagellar Filament
Authors: Ely Bert , Ely Tracey W. , Crymes William B. , Minnich Scott A. 
Published: July 2002

ABSTRACT

The
Caulobacter crescentus
flagellar filament is assembled from multiple flagellin proteins that are encoded by six genes. The amino acid sequences of the FljJ and FljL flagellins are divergent from those of the other four flagellins. Since these flagellins are the first to be assembled in the flagellar filament, one or both might have specialized to facilitate the initiation of filament assembly.
Reduction of GC → TA Transversion Mutation by Overexpression of MutS in
Escherichia coli
K-12
Authors: Zhao Jingyong , Winkler Malcolm E. 
Published: July 2002

ABSTRACT

Overexpression of the MutS repair protein significantly decreased the rate of
lacZ
GC → TA transversion mutation in stationary-phase and exponentially growing bacteria and in
mutY
and
mutM
mutants, which accumulate mismatches between 8-oxoguanine (8-oxoG) and adenine residues in DNA. Conversely, GC → TA transversion increased in
mutL
or
mutS
mutants in stationary phase. In contrast, overexpression of MutS did not appreciably reduce
lacZ
AT → CG transversion mutation in a
mutT
mutant. These results suggest that MutS-dependent repair can correct 8-oxoG:A mismatches in
Escherichia coli
cells but may not be able to compete with mutation fixation by MutY in
mutT
mutants.
Aerotolerance and Peroxide Resistance in Peroxidase and PerR Mutants of
Streptococcus pyogenes
Authors: King Katherine Y. , Horenstein Joshua A. , Caparon Michael G. 
Published: July 2002

ABSTRACT

Survival in aerobic conditions is critical to the pathogenicity of many bacteria. To investigate the means of aerotolerance and resistance to oxidative stress in the catalase-negative organism
Streptococcus pyogenes
, we used a genomics-based approach to identify and inactivate homologues of two peroxidase genes, encoding alkyl hydroperoxidase (
ahpC
) and glutathione peroxidase (
gpoA
). Single and double mutants survived as well as the wild type under aerobic conditions. However, they were more susceptible than the wild type to growth suppression by paraquat and cumene hydroperoxide. In addition, we show that
S. pyogenes
demonstrates an inducible peroxide resistance response when treated with sublethal doses of peroxide. This resistance response was intact in
ahpC
and
gpoA
mutants but not in mutants lacking PerR, a repressor of several genes including
ahpC
and catalase (
katA
) in
Bacillus subtilis
. Because our data indicate that these peroxidase genes are not essential for aerotolerance or induced resistance to peroxide stress in
S. pyogenes
, genes for a novel mechanism of managing peroxide stress may be regulated by PerR in streptococci.
HbpR, a New Member of the XylR/DmpR Subclass within the NtrC Family of Bacterial Transcriptional Activators, Regulates Expression of 2-Hydroxybiphenyl Metabolism in
Pseudomonas azelaica
HBP1
Authors: Jaspers Marco C. M. , Suske Winfried A. , Schmid Andreas , Goslings David A. M. , Kohler Hans-Peter E. , van der Meer Jan Roelof 
Published: July 2002

ABSTRACT

The regulation of 2-hydroxybiphenyl and 2,2′-dihydroxybiphenyl degradation in
Pseudomonas azelaica
is mediated by the regulatory gene,
hbpR
. The
hbpR
gene encodes a 63-kDa protein belonging to the NtrC family of prokaryotic transcriptional activators and having the highest homology to members of the XylR/DmpR subclass. Disruption of the
hbpR
gene in
P. azelaica
and complementation in
trans
showed that the HbpR protein was the key regulator for 2-hydroxybiphenyl metabolism. Induction experiments with
P. azelaica
and
Escherichia coli
containing
luxAB
-based transcriptional fusions revealed that HbpR activates transcription from a promoter (P

hbpC

) in front of the first gene for 2-hydroxybiphenyl degradation,
hbpC
, and that 2-hydroxybiphenyl itself is the direct effector for HbpR-mediated activation. Of several compounds tested, only the pathway substrates 2-hydroxybiphenyl and 2,2′-dihydroxybiphenyl and structural analogs like 2-aminobiphenyl and 2-hydroxybiphenylmethane were effectors for HbpR activation. HbpR is therefore, to our knowledge, the first regulator of the XylR/DmpR class that recognizes biaromatic but not monoaromatic structures. Analysis of a spontaneously occurring mutant,
P. azelaica
HBP1 Prp, which can grow with the non-wild-type effector 2-propylphenol, revealed a single mutation in the
hbpR
gene (T613C) leading to a Trp→Arg substitution at amino acid residue 205.
P. azelaica
HBP1 derivative strains without a functional
hbpR
gene constitutively expressed the genes for 2-hydroxybiphenyl degradation when complemented in
trans
with the
hbpR
-T613C gene. This suggests the importance of this residue, which is conserved among all members of the XylR/DmpR subclass, for interdomain repression.
Identification and Characterization of a New Prespore-Specific Regulatory Gene,
rsfA
, of
Bacillus subtilis
Authors: Juan Wu Ling , Errington Jeff 
Published: July 2002

ABSTRACT

Differential gene expression during
Bacillus subtilis
sporulation is controlled by sigma factors and other regulatory effectors. The first compartmentalized sigma factor, ς
F
, is active specifically in the prespore compartment. During our screening for new chromosome segregation mutants using a ς
F
-dependent
gpr-lacZ
reporter as a probe, we identified a new gene (
ywfN
) required for maximal expression of the reporter and named it
rsfA
. The product of
rsfA
has features of gene regulatory proteins, and the protein colocalizes with DNA. The expression of
rsfA
is under the control of both ς
F
and ς
G
. Null mutations in
rsfA
have different effects on the expression of ς
F
-dependent genes, suggesting that the RsfA protein is a regulator of transcription that fine-tunes gene expression in the prespore.
Hydrogen Peroxide Activates the SoxRS Regulon In Vivo
Authors: Manchado Manuel , Michán Carmen , Pueyo Carmen 
Published: July 2002

ABSTRACT

By multiplex reverse transcription-PCR, we demonstrate that the SoxRS response, which protects cells against superoxide toxicity, is triggered also by hydrogen peroxide. SoxR-dependent inductions of 7.3-, 7.6-, 4.6-, 2.2-, and 2.6-fold were quantified for
soxS
,
micF
,
sodA
,
inaA
, and
fpr
transcripts, respectively. This finding suggests an extensive and tight connectivity between different regulatory pathways in the
Escherichia coli
response to oxidative stress.
Membrane Redistribution of the
Escherichia coli
MinD Protein Induced by MinE
Authors: Rowland S. L. , Fu X. , Sayed M. A. , Zhang Y. , Cook W. R. , Rothfield L. I. 
Published: July 2002

ABSTRACT

Escherichia coli
cells contain potential division sites at midcell and adjacent to the cell poles. Selection of the correct division site at midcell is controlled by three proteins: MinC, MinD, and MinE. It has previously been shown (D. Raskin and P. de Boer, Cell 91:685–694, 1997) that MinE-Gfp localizes to the midcell site in an MinD-dependent manner. We use here Gfp-MinD to show that MinD associates with the membrane around the entire periphery of the cell in the absence of the other Min proteins and that MinE is capable of altering the membrane distribution pattern of Gfp-MinD. Studies with the isolated N-terminal and C-terminal MinE domains indicated different roles for the two MinE domains in the redistribution of membrane-associated MinD.
Alteration of the Lipopolysaccharide Structure Affects the Functioning of the Xcp Secretory System in
Pseudomonas aeruginosa
Authors: Michel Gérard , Ball Geneviève , Goldberg Joanna B. , Lazdunski Andrée 
Published: July 2002

ABSTRACT

Pseudomonas aeruginosa
secretes a wide range of hydrolytic enzymes into the external medium by the Xcp secretion machinery. To better understand the role played by envelope constituents in the functioning of this type II secretory system, we have studied the influence of lipopolysaccharide (LPS) on the secretion of two extracellular enzymes, the elastase LasB and the lipase LipA. Strains with defective LPS decreased production of LasB and altered the secretion processes of both LasB and LipA without any apparent effect on the composition of the Xcp machinery. The PAO1
algC
strain, defective in the outer core of LPS, was leaky, as shown by the extracellular release of the periplasmic β-lactamase. Generation of an
xcpR
mutation in this mutant led only to a partial accumulation of LasB within the cells, indicating that in strain PAO1
algC
with a functional
xcpR
gene, LasB was released in the extracellular medium partly by leakage and partly by secretion. The pool of LasB released into the medium by leakage was not recovered in an active form, while extracellular LasB was active when secreted via the secretory machinery. Further analysis revealed that the presence of a functional Xcp machinery is strictly required for the activation process of LasB. Our results provide evidence that the Xcp system is not fully functional when the LPS structure of
P. aeruginosa
is altered.
Functional Domains of the TOL Plasmid Transcription Factor XylS
Authors: Kaldalu Niilo , Toots Urve , de Lorenzo Victor , Ustav Mart 
Published: July 2002

ABSTRACT

The alkylbenzoate degradation genes of
Pseudomonas putida
TOL plasmid are positively regulated by XylS, an AraC family protein, in a benzoate-dependent manner. In this study, we used deletion mutants and hybrid proteins to identify which parts of XylS are responsible for the DNA binding, transcriptional activation, and benzoate inducibility. We found that a 112-residue C-terminal fragment of XylS binds specifically to the
Pm
operator in vitro, protects this sequence from DNase I digestion identically to the wild-type (wt) protein, and activates the
Pm
promoter in vivo. When overexpressed, that C-terminal fragment could activate transcription as efficiently as wt XylS. All the truncations, which incorporated these 112 C-terminal residues, were able to activate transcription at least to some extent when overproduced. Intactness of the 210-residue N-terminal portion was found to be necessary for benzoate responsiveness of XylS. Deletions in the N-terminal and central regions seriously reduced the activity of XylS and caused the loss of effector control, whereas insertions into the putative interdomain region did not change the basic features of the XylS protein. Our results confirm that XylS consists of two parts which probably interact with each other. The C-terminal domain carries DNA-binding and transcriptional activation abilities, while the N-terminal region carries effector-binding and regulatory functions.
Genetic and Biochemical Characterization of
Salmonella enterica
Serovar Typhi Deoxyribokinase
Authors: Tourneux Lise , Bucurenci Nadia , Saveanu Cosmin , Kaminski Pierre Alexandre , Bouzon Madeleine , Pistotnik Elisabeth , Namane Abdelkader , Marlière Philippe , Bârzu Octavian , Li de la Sierra Inès , Neuhard Jan , Gilles Anne-Marie 
Published: July 2002

ABSTRACT

We identified in the genome of
Salmonella enterica
serovar Typhi the gene encoding deoxyribokinase,
deoK
. Two other genes, vicinal to
deoK
, were determined to encode the putative deoxyribose transporter (
deoP
) and a repressor protein (
deoQ
). This locus, located between the
uhpA
and
ilvN
genes, is absent in
Escherichia coli
. The
deoK
gene inserted on a plasmid provides a selectable marker in
E. coli
for growth on deoxyribose-containing medium. Deoxyribokinase is a 306-amino-acid protein which exhibits about 35% identity with ribokinase from serovar Typhi,
S. enterica
serovar Typhimurium, or
E. coli
. The catalytic properties of the recombinant deoxyribokinase overproduced in
E. coli
correspond to those previously described for the enzyme isolated from serovar Typhimurium. From a sequence comparison between serovar Typhi deoxyribokinase and
E. coli
ribokinase, whose crystal structure was recently solved, we deduced that a key residue differentiating ribose and deoxyribose is Met10, which in ribokinase is replaced by Asn14. Replacement by site-directed mutagenesis of Met10 with Asn decreased the
V
max
of deoxyribokinase by a factor of 2.5 and increased the
K
m
for deoxyribose by a factor of 70, compared to the parent enzyme.
Substrate Range and Genetic Analysis of
Acinetobacter
Vanillate Demethylase
Authors: Morawski Birgit , Segura Ana , Ornston L. Nicholas 
Published: July 2002

ABSTRACT

An
Acinetobacter
sp. genetic screen was used to probe structure-function relationships in vanillate demethylase, a two-component monooxygenase. Mutants with null, leaky, and heat-sensitive phenotypes were isolated. Missense mutations tended to be clustered in specific regions, most of which make known contributions to catalytic activity. The vanillate analogs
m
-anisate,
m
-toluate, and 4-hydroxy-3,5-dimethylbenzoate are substrates of the enzyme and weakly inhibit the metabolism of vanillate by wild-type
Acinetobacter
bacteria. PCR mutagenesis of
vanAB
, followed by selection for strains unable to metabolize vanillate, yielded mutant organisms in which vanillate metabolism is more strongly inhibited by the vanillate analogs. Thus, the procedure opens for investigation amino acid residues that may contribute to the binding of either vanillate or its chemical analogs to wild-type and mutant vanillate demethylases. Selection of phenotypic revertants following PCR mutagenesis gave an indication of the extent to which amino acid substitutions can be tolerated at specified positions. In some cases, only true reversion to the original amino acid was observed. In other examples, a range of amino acid substitutions was tolerated. In one instance, phenotypic reversion failed to produce a protein with the original wild-type sequence. In this example, constraints favoring certain nucleotide substitutions appear to be imposed at the DNA level.
Identification of the Active Site of HetR Protease and Its Requirement for Heterocyst Differentiation in the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Dong Yuqing , Huang Xu , Wu Xiang-Yu , Zhao Jindong 
Published: July 2002

ABSTRACT

HetR is a serine-type protease required for heterocyst differentiation in heterocystous cyanobacteria under conditions of nitrogen deprivation. We have identified the active Ser residue of HetR from
Anabaena
sp. strain PCC 7120 by site-specific mutagenesis. By changing the S152 residue to an Ala residue, the mutant protein cannot be labeled by Dansyl fluoride, a specific serine-type protein inhibitor. The mutant protein showed no autodegradation in vitro. The mutant
hetR
gene was introduced into
Anabaena
strain 884a, a
hetR
mutant. The resultant strain,
Anabaena
strain S152A, could not form heterocysts under conditions of nitrogen deprivation even though the up-regulation of the mutant
hetR
gene was induced upon removal of combined nitrogen. The
Anabaena
strain 216, which carries a mutant
hetR
gene encoding S179N HetR and could not form heterocysts, also produced HetR protein upon induction. Sequence comparison shows that Ser152 is conserved in all cyanobacterial HetR. Immunoblotting was used to study HetR induction in both the wild-type and mutant strains. The amount of mutant HetR in strain S152A and in strain 216 increased continuously for 24 h after nitrogen step-down, while the amount of HetR in wild-type cells reached a maximum level within 6 h after nitrogen step-down. Our results show the Ser152 is the active site of HetR. The protease activity is required for heterocyst differentiation and might be needed for repression of HetR overproduction under conditions of nitrogen deprivation.
Activation of SoxR by Overproduction of Desulfoferrodoxin: Multiple Ways To Induce the
soxRS
Regulon
Authors: Gaudu Philippe , Dubrac Sarah , Touati Danièle 
Published: July 2002

ABSTRACT

The
soxRS
response, which protects cells against superoxide toxicity, is triggered by the oxidation of SoxR, a transcription factor. Superoxide excess and NADPH depletion induce the regulon. Unexpectedly, we found that the overproduction of desulfoferrodoxin, a superoxide reductase from sulfate-reducing bacteria, also induced this response. We suggest that desulfoferrodoxin interferes with the reducing pathway that keeps SoxR in its inactive form.
Mobilization of Plasmids and Chromosomal DNA Mediated by the SXT Element, a Constin Found in
Vibrio cholerae
O139
Authors: Hochhut Bianca , Marrero Joeli , Waldor Matthew K. 
Published: July 2002

ABSTRACT

The
Vibrio cholerae
SXT element encodes resistance to multiple antibiotics and is a conjugative, self-transmissible, and chromosomally integrating element (a constin). Excision and self-transfer of the SXT element require an element-encoded integrase. We now report that the SXT element can also mobilize the plasmids RSF1010 and CloDF13 in
trans
as well as chromosomal DNA in an Hfr-like manner. SXT element-mediated mobilization of plasmids and chromosomal DNA, unlike its self-transfer, is not dependent upon excision of the element from the chromosome. These results raise the possibility that the SXT element and other constins play a general role in horizontal gene transfer among gram-negative bacteria.
RegG, a CcpA Homolog, Participates in Regulation of Amylase-Binding Protein A Gene (
abpA
) Expression in
Streptococcus gordonii
Authors: Rogers Jeffrey D. , Scannapieco Frank A. 
Published: July 2002

ABSTRACT

The amylase-binding protein A (AbpA) of
Streptococcus gordonii
was found to be undetectable in supernatants of mid-log-phase cultures containing >1% glucose but abundant in supernatants of cultures made with brain heart infusion (BHI), which contains 0.2% glucose. A 10-fold decrease in the level of
abpA
mRNA in
S. gordonii
cells cultured in BHI was noted after the addition of glucose to 1%. Analysis of the
abpA
sequence revealed a potential catabolite responsive element CRE 153 bp downstream of the putative translational start site. A catabolite control protein A gene (
ccpA
) homolog from
S. gordonii
, designated
regG
, was cloned. A
regG
mutant strain demonstrated moderately less repression of
abpA
transcription in the presence of 1% glucose. Diauxic growth with glucose and lactose was not affected in the RegG mutant compared to the wild-type parental strain. These results suggest that while RegG plays a role in
abpA
expression, other mechanisms of catabolite repression are present.
Anatomical Analysis of
Saccharomyces cerevisiae
Stalk-Like Structures Reveals Spatial Organization and Cell Specialization
Authors: Scherz Ruth , Shinder Vera , Engelberg David 
Published: July 2002

ABSTRACT
Recently we reported an unusual multicellular organization in yeast that we termed stalk-like structures. These structures are tall (0.5 to 3 cm long) and narrow (1 to 3 mm in diameter). They are formed in response to UV radiation of cultures spread on high agar concentrations. Here we present an anatomical analysis of the stalks. Microscopic inspection of cross sections taken from stalks revealed that stalks are composed of an inner core in which cells are dense and vital and a layer of cells (four to six rows) that surrounds the core. This outer layer is physically separated from the core and contains many dead cells. The outer layer may form a protective shell for the core cells. Through electron microscopy analysis we observed three types of cells within the stalk population: (i) cells containing many unusual vesicles, which might be undergoing some kind of cell death; (ii) cells containing spores (usually one or two spores only); and (iii) familiar rounded cells. We suggest that stalk cells are not only spatially organized but may undergo processes that induce a certain degree of cell specialization. We also show that high agar concentration alone, although not sufficient to induce stalk formation, induces dramatic changes in a colony's morphology. Most striking among the agar effects is the induction of growth into the agar, forming peg-like structures. Colonies grown on 4% agar or higher are reminiscent of stalks in some aspects. The agar concentration effects are mediated in part by the Ras pathway and are related to the invasive-growth phenomenon.
Cytochrome Complex Essential for Photosynthetic Oxidation of both Thiosulfate and Sulfide in
Rhodovulum sulfidophilum
Authors: Appia-Ayme Corinne , Little Phillip J. , Matsumoto Yumi , Leech Andrew P. , Berks Ben C. 
Published: July 2002

ABSTRACT

Many photosynthetic bacteria use inorganic sulfur compounds as electron donors for carbon dioxide fixation. A thiosulfate-induced cytochrome
c
has been purified from the photosynthetic α-proteobacterium
Rhodovulum sulfidophilum
. This cytochrome
c
551
is a heterodimer of a diheme 30-kDa SoxA subunit and a monoheme 15-kDa SoxX subunit. The cytochrome
c
551
structural genes are part of an 11-gene
sox
locus. Sequence analysis suggests that the ligands to the heme iron in SoxX are a methionine and a histidine, while both SoxA hemes are predicted to have unusual cysteine-plus-histidine coordination. A
soxA
mutant strain is unable to grow photoautotrophically on or oxidize either thiosulfate or sulfide. Cytochrome
c
551
is thus essential for the metabolism of both these sulfur species. Periplasmic extracts of wild-type
R. sulfidophilum
exhibit thiosulfate:cytochrome
c
oxidoreductase activity. However, such activity can only be measured for a
soxA
mutant strain if the periplasmic extract is supplemented with purified cytochrome c
551
. Gene clusters similar to the
R. sulfidophilum sox
locus can be found in the genome of a green sulfur bacterium and in phylogenetically diverse nonphotosynthetic autotrophs.