bluuebunny/crossref_metadata_2025_split huggingface dataset:
LuxR- and Acyl-Homoserine-Lactone-Controlled Non-
lux
Genes Define a Quorum-Sensing Regulon in
Vibrio fischeri
Authors: Callahan Sean M. , Dunlap Paul V. 
Published: July 2002

ABSTRACT

The luminescence (
lux
) operon (
luxICDABEG
) of the symbiotic bacterium
Vibrio fischeri
is regulated by the transcriptional activator LuxR and two acyl-homoserine lactone (acyl-HSL) autoinducers (the
luxI
-dependent 3-oxo-hexanoyl-HSL [3-oxo-C6-HSL] and the
ainS
-dependent octanoyl-HSL [C8-HSL]) in a population density-responsive manner called quorum sensing. To identify quorum-sensing-regulated (QSR) proteins different from those encoded by
lux
genes, we examined the protein patterns of
V. fischeri
quorum-sensing mutants defective in
luxI
,
ainS
, and
luxR
by two-dimensional polyacrylamide gel electrophoresis. Five non-Lux QSR proteins, QsrP, RibB, AcfA, QsrV, and QSR 7, were identified; their production occurred preferentially at high population density, required both LuxR and 3-oxo-C6-HSL, and was inhibited by C8-HSL at low population density. The genes encoding two of the QSR proteins were characterized:
qsrP
directs cells to synthesize an apparently novel periplasmic protein, and
ribB
is a homolog of the
Escherichia coli
gene for 3,4-dihydroxy-2-butanone 4-phosphate synthase, a key enzyme for riboflavin synthesis. The
qsrP
and
ribB
promoter regions each contained a sequence similar to the
lux
operon
lux
box, a 20-bp region of dyad symmetry necessary for LuxR/3-oxo-C6-HSL-dependent activation of
lux
operon transcription.
V. fischeri qsrP
and
ribB
mutants exhibited no distinct phenotype in culture. However, a
qsrP
mutant, in competition with its parent strain, was less successful in colonizing
Euprymna scolopes
, the symbiotic host of
V. fischeri
. The newly identified QSR genes, together with the
lux
operon, define a LuxR/acyl-HSL-responsive quorum-sensing regulon in
V. fischeri.
A Mutation in
secY
That Causes Enhanced SecA Insertion and Impaired Late Functions in Protein Translocation
Authors: Matsumoto Gen , Homma Takayuki , Mori Hiroyuki , Ito Koreaki 
Published: July 2002

ABSTRACT

A cold-sensitive
secY
mutant (
secY125
) with an amino acid substitution in the first periplasmic domain causes in vivo retardation of protein export. Inverted membrane vesicles prepared from this mutant were as active as the wild-type membrane vesicles in translocation of a minute amount of radioactive preprotein. The mutant membrane also allowed enhanced insertion of SecA, and this SecA insertion was dependent on the SecD and SecF functions. These and other observations suggested that the early events in translocation, such as SecA-dependent insertion of the signal sequence region, is actually enhanced by the SecY125 alteration. In contrast, since the mutant membrane vesicles had decreased capacity to translocate chemical quantity of pro-OmpA and since they were readily inactivated by pretreatment of the vesicles under the conditions in which a pro-OmpA translocation intermediate once accumulated, the late translocation functions appear to be impaired. We conclude that this periplasmic
secY
mutation causes unbalanced early and late functions in translocation, compromising the translocase's ability to catalyze multiple rounds of reactions.
Glucose Transporter Mutants of
Escherichia coli
K-12 with Changes in Substrate Recognition of IICB
Glc
and Induction Behavior of the
ptsG
Gene
Authors: Zeppenfeld Tim , Larisch Christina , Lengeler Joseph W. , Jahreis Knut 
Published: July 2002

ABSTRACT

In
Escherichia coli
K-12, the major glucose transporter with a central role in carbon catabolite repression and in inducer exclusion is the phosphoenolpyruvate-dependent glucose:phosphotransferase system (PTS). Its membrane-bound subunit, IICB
Glc
, is encoded by the gene
ptsG
; its soluble domain, IIA
Glc
, is encoded by
crr
, which is a member of the
pts
operon. The system is inducible by
d
-glucose and, to a lesser degree, by
l
-sorbose. The regulation of
ptsG
transcription was analyzed by testing the induction of IICB
Glc
transporter activity and of a single-copy Φ(
ptsGop-lacZ
) fusion. Among mutations found to affect directly
ptsG
expression were those altering the activity of adenylate cyclase (
cyaA
), the repressor DgsA (
dgsA
; also called Mlc), the general PTS proteins enzyme I (
ptsI
) and histidine carrier protein HPr (
ptsH
), and the IIA
Glc
and IIB
Glc
domains, as well as several authentic and newly isolated UmgC mutations. The latter, originally thought to map in the repressor gene
umgC
outside the
ptsG
locus, were found to represent
ptsG
alleles. These affected invariably the substrate specificity of the IICB
Glc
domain, thus allowing efficient transport and phosphorylation of substrates normally transported very poorly or not at all by this PTS. Simultaneously, all of these substrates became inducers for
ptsG
. From the analysis of the mutants, from
cis-trans
dominance tests, and from the identification of the amino acid residues mutated in the UmgC mutants, a new regulatory mechanism involved in
ptsG
induction is postulated. According to this model, the phosphorylation state of IIB
Glc
modulates IIC
Glc
which, directly or indirectly, controls the repressor DgsA and hence
ptsG
expression. By the same mechanism, glucose uptake and phosphorylation also control the expression of the
pts
operon and probably of all operons controlled by the repressor DgsA.
A Large Gene Cluster for the
Clostridium cellulovorans
Cellulosome
Authors: Tamaru Yutaka , Karita Shuichi , Ibrahim Atef , Chan Helen , Doi Roy H. 
Published: July 2002

ABSTRACT

A large gene cluster for the
Clostridium cellulovorans
cellulosome has been cloned and sequenced upstream and downstream of the
cbpA
and
exgS
genes (C.-C. Liu and R. H. Doi, Gene 211:39–47, 1998). Gene walking revealed that the
engL
gene cluster (Y. Tamaru and R. H. Doi, J. Bacteriol. 182:244–247, 2000) was located downstream of the
cbpA-exgS
genes. Further DNA sequencing revealed that this cluster contains the genes for the scaffolding protein CbpA, the exoglucanase ExgS, several endoglucanases of family 9, the mannanase ManA, and the hydrophobic protein HbpA containing a surface layer homology domain and a hydrophobic (or cohesin) domain. The sequence of the clustered genes is
cbpA-exgS-engH-engK-hbpA-engL-manA-engM-engN
and is about 22 kb in length. The
engN
gene did not have a complete catalytic domain, indicating that
engN
is a truncated gene. This large gene cluster is flanked at the 5′ end by a putative noncellulosomal operon consisting of
nifV-orf1-sigX-regA
and at the 3′ end by noncellulosomal genes with homology to transposase (
trp
) and malate permease (
mle
). Since gene clusters for the cellulosome are also found in
C. cellulolyticum
and
C. josui
, they seem to be typical of mesophilic clostridia, indicating that the large gene clusters may arise from a common ancestor with some evolutionary modifications.
OmpR Regulates the Two-Component System SsrA-SsrB in
Salmonella
Pathogenicity Island 2
Authors: Lee Anthea K. , Detweiler Corrella S. , Falkow Stanley 
Published: July 2002

ABSTRACT

Salmonella
pathogenicity island 2 (SPI-2) encodes a putative, two-component regulatory system, SsrA-SsrB, which regulates a type III secretion system needed for replication inside macrophages and systemic infection in mice. The sensor and regulator homologs,
ssrAB
(
spiR
), and genes within the secretion system, including the structural gene
ssaH
, are transcribed after
Salmonella
enters host cells. We have studied the transcriptional regulation of
ssrAB
and the secretion system by using
gfp
fusions to the
ssrA
and
ssaH
promoters. We found that early transcription of
ssrA
, after entry into macrophages, is most efficient in the presence of OmpR. An
ompR
mutant strain does not exhibit replication within cultured macrophages. Furthermore, footprint analysis shows that purified OmpR protein binds directly to the
ssrA
promoter region. We also show that minimal medium, pH 4.5, induces SPI-2 gene expression in wild-type but not
ompR
mutant strains. We conclude that the type III secretion system of SPI-2 is regulated by OmpR, which activates expression of
ssrA
soon after
Salmonella
enters the macrophage.
Isolation of an Inner Membrane-Derived Subfraction That Supports In Vitro Replication of a Mini-RK2 Plasmid in
Escherichia coli
Authors: Kim Peter D. , Firshein William 
Published: July 2002

ABSTRACT

Previous results have demonstrated that the inner, but not the outer, membrane fraction of
Escherichia coli
is the site of membrane-associated DNA replication of plasmid RK2, a broad-host-range plasmid capable of replication in a wide variety of gram-negative hosts (K. Michaels, J. Mei, and W. Firshein, Plasmid 32:19–31, 1994). To resolve the inner membrane replication site further, the procedure of Ishidate et al. (K. Ishidate, E. S. Creeger, J. Zrike, S. Deb, G. Glauner, T. J. MacAlister, and L. I. Rothfield, J. Biol. Chem. 261:428–443, 1986) was used to separate the inner membrane into a number of subfractions, of which only one, a small subfraction containing only 10% of the entire membrane, was found to synthesize DNA inhibited by antibody prepared against the plasmid-encoded initiation protein TrfA. This is the same subfraction that was also found to bind
oriV
and TrfA to the greatest extent in filter binding assays (J. Mei, S. Benashski, and W. Firshein, J. Bacteriol. 177:6766–6772, 1995).
The
Yersinia pestis
YscY Protein Directly Binds YscX, a Secreted Component of the Type III Secretion Machinery
Authors: Day James B. , Plano Gregory V. 
Published: July 2002

ABSTRACT

Human pathogenic yersiniae organisms export and translocate the Yop virulence proteins and V antigen upon contact with a eukaryotic cell.
Yersinia pestis
mutants defective for production of YscX or YscY were unable to export the Yops and V antigen. YscX and YscY were both present in the
Y. pestis
cell pellet fraction; however, YscX was also found in the culture supernatant. YscY showed structural and amino acid sequence similarities to the Syc family of proteins. YscY specifically recognized and bound to a region of YscX that included a predicted coiled-coil region. These data suggest that YscY may function as a chaperone for YscX in
Y. pestis.
Oxaloacetate Synthesis in the Methanarchaeon
Methanosarcina barkeri
: Pyruvate Carboxylase Genes and a Putative
Escherichia coli
-Type Bifunctional Biotin Protein Ligase Gene (
bpl/birA
) Exhibit a Unique Organization
Authors: Mukhopadhyay Biswarup , Purwantini Endang , Kreder Cynthia L. , Wolfe Ralph S. 
Published: July 2002

ABSTRACT

Evidence is presented that, in
Methanosarcina barkeri
oxaloacetate synthesis, an essential and major CO
2
fixation reaction is catalyzed by an apparent α
4
β
4
-type acetyl coenzyme A-independent pyruvate carboxylase (PYC), composed of 64.2-kDa biotinylated and 52.9-kDa ATP-binding subunits. The purified enzyme was most active at 70°C, insensitive to aspartate and glutamate, mildly inhibited by α-ketoglutarate, and severely inhibited by ATP, ADP, and excess Mg
2+
. It showed negative cooperativity towards bicarbonate at 70°C but not at 37°C. The organism expressed holo-PYC without an external supply of biotin and, thus, synthesized biotin.
pycA, pycB
, and a putative
bpl
gene formed a novel operon-like arrangement. Unlike other archaeal homologs, the putative biotin protein ligases (BPLs) of
M. barkeri
and the closely related euryarchaeon
Archaeoglobus fulgidus
appeared to be of the
Escherichia coli
-type (bifunctional, with two activities: BirA or a repressor of the biotin operon and BPL). We found the element Tyr(Phe)Pro
X
5
Phe(Tyr) to be fully conserved in biotin-dependent enzymes; it might function as the hinge for their “swinging arms.”
Localization of NAD(P)H Dehydrogenase in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803
Authors: Ohkawa Hiroshi , Sonoda Masatoshi , Shibata Mari , Ogawa Teruo 
Published: July 2002

ABSTRACT

Antibodies raised against NdhH and NdhB detected these proteins in the thylakoid membrane of
Synechocystis
sp. strain PCC 6803, but not in a purified cytoplasmic membrane. We conclude that NAD(P)H dehydrogenase is largely, if not exclusively, confined to the thylakoid membrane.
Microaerophilic Induction of the Alpha-Crystallin Chaperone Protein Homologue (
hspX
) mRNA of
Mycobacterium tuberculosis
Authors: DesJardin Lucy E. , Hayes LaDonna G. , Sohaskey Charles D. , Wayne Lawrence G. , Eisenach Kathleen D. 
Published: July 2002

ABSTRACT

Among the products that are expressed when
Mycobacterium tuberculosis
undergoes hypoxic shiftdown to nonreplicating persistence (NRP) is the alpha-crystallin chaperone protein homologue (Acr). This expression coincides with the previously reported appearance of a respiratory type of nitrate reductase activity, the increase in glycine dehydrogenase activity, and the production of a unique antigen, URB-1. In a timed sampling study, using a slowly stirred oxygen depletion culture model, we have demonstrated that the
hspX
mRNA that codes for Acr protein as well as the protein itself is induced just as the bacilli enter the microaerophilic NRP stage 1 (NRP-1). In contrast to the induction observed for
hspX
mRNA, levels of 16S rRNA,
fbpB
mRNA (encoding the 85B alpha antigen), and
aroB
mRNA (encoding dehydroquinate synthase) demonstrate relatively small to no change upon entering NRP-1. Acr protein was shown to be identical to URB-1 by Western analysis with anti-URB-1 antibody. The fact that antibody to Acr is found in a high percentage of tuberculosis patients suggests that the hypoxic shiftdown of tubercle bacilli to the NRP state that occurs in vitro, resulting in production of the alpha-crystallin protein, occurs in vivo as well. Simultaneous abrupt increases in
hspX
mRNA and Acr protein suggest that Acr protein expression is controlled at the level of transcription.
Genetics and Regulation of Chitobiose Utilization in
Borrelia burgdorferi
Authors: Tilly Kit , Elias Abdallah F. , Errett Jennifer , Fischer Elizabeth , Iyer Radha , Schwartz Ira , Bono James L. , Rosa Patricia 
Published: July 2002

ABSTRACT

Borrelia burgdorferi
spends a significant proportion of its life cycle within an ixodid tick, which has a cuticle containing chitin, a polymer of
N
-acetylglucosamine (GlcNAc). The
B. burgdorferi celA
,
celB
, and
celC
genes encode products homologous to transporters for cellobiose and chitobiose (the dimer subunit of chitin) in other bacteria, which could be useful for bacterial nutrient acquisition during growth within ticks. We found that chitobiose efficiently substituted for GlcNAc during bacterial growth in culture medium. We inactivated the
celB
gene, which encodes the putative membrane-spanning component of the transporter, and compared growth of the mutant in various media to that of its isogenic parent. The mutant was no longer able to utilize chitobiose, while neither the mutant nor the wild type can utilize cellobiose. We propose renaming the three genes
chbA
,
chbB
, and
chbC
, since they probably encode a chitobiose transporter. We also found that the
chbC
gene was regulated in response to growth temperature and during growth in medium lacking GlcNAc.
Degradation of Host Heme Proteins by Lysine- and Arginine-Specific Cysteine Proteinases (Gingipains) of
Porphyromonas gingivalis
Authors: Sroka Aneta , Sztukowska Maryta , Potempa Jan , Travis James , Genco Caroline Attardo 
Published: July 2002

ABSTRACT

Porphyromonas gingivalis
can use hemoglobin bound to haptoglobin and heme complexed to hemopexin as heme sources; however, the mechanism by which hemin is released from these proteins has not been defined. In the present study, using a variety of analytical methods, we demonstrate that lysine-specific cysteine proteinase of
P. gingivalis
(gingipain K, Kgp) can efficiently cleave hemoglobin, hemopexin, haptoglobin, and transferrin. Degradation of hemopexin and transferrin in human serum by Kgp was also detected; however, we did not observe extensive degradation of hemoglobin in serum by Kgp. Likewise the β-chain of haptoglobin was partially protected from degradation by Kgp in a haptoglobin-hemoglobin complex. Arginine-specific gingipains (gingipains R) were also found to degrade hemopexin and transferrin in serum; however, this was observed only at relatively high concentrations of these enzymes. Growth of
P. gingivalis
strain A7436 in a minimal media with normal human serum as a source of heme correlated not only with the ability of the organism to degrade hemoglobin, haptoglobin, hemopexin, and transferrin but also with an increase in gingipain K and gingipain R activity. The ability of gingipain K to cleave hemoglobin, haptoglobin, and hemopexin may provide
P. gingivalis
with a useable source of heme for growth and may contribute to the proliferation of
P. gingivalis
within periodontal pockets in which erythrocytes are abundant.
Characterization of Xylanolytic Enzymes in
Clostridium cellulovorans
: Expression of Xylanase Activity Dependent on Growth Substrates
Authors: Kosugi Akihiko , Murashima Koichiro , Doi Roy H. 
Published: July 2002

ABSTRACT

Xylanase activity of
Clostridium cellulovorans
, an anaerobic, mesophilic, cellulolytic bacterium, was characterized. Most of the activity was secreted into the growth medium when the bacterium was grown on xylan. Furthermore, when the extracellular material was separated into cellulosomal and noncellulosomal fractions, the activity was present in both fractions. Each of these fractions contained at least two major and three minor xylanase activities. In both fractions, the pattern of xylan hydrolysis products was almost identical based on thin-layer chromatography analysis. The major xylanase activities in both fractions were associated with proteins with molecular weights of about 57,000 and 47,000 according to zymogram analyses, and the minor xylanases had molecular weights ranging from 45,000 to 28,000. High α-arabinofuranosidase activity was detected exclusively in the noncellulosomal fraction. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that cellulosomes derived from xylan-, cellobiose-, and cellulose-grown cultures had different subunit compositions. Also, when xylanase activity in the cellulosomes from the xylan-grown cultures was compared with that of cellobiose- and cellulose-grown cultures, the two major xylanases were dramatically increased in the presence of xylan. These results strongly indicated that
C. cellulovorans
is able to regulate the expression of xylanase activity and to vary the cellulosome composition depending on the growth substrate.
Interplay between the Specific Chaperone-Like Proteins HybG and HypC in Maturation of Hydrogenases 1, 2, and 3 from
Escherichia coli
Authors: Blokesch Melanie , Magalon Axel , Böck August 
Published: July 2002

ABSTRACT

The
hybG
gene product from
Escherichia coli
has been identified as a chaperone-like protein acting in the maturation of hydrogenases 1 and 2. It was shown that HybG forms a complex with the precursor of the large subunit of hydrogenase 2. As with HypC, which is the chaperone-like protein involved in hydrogenase 3 maturation, the N-terminal cysteine residue is crucial for complex formation. Introduction of a deletion into
hybG
abolished the generation of active hydrogenase 2 but only quantitatively reduced hydrogenase 1 activity since HypC could replace HybG in this function. In contrast, HybG could not take over the role of HypC in a Δ
hypC
genetic background. Overproduction of HybG, especially of the variants with the replaced N-terminal cysteine residue, strongly interfered with hydrogenase 3 maturation, apparently by titrating some other component(s) of the maturation machinery. The results indicate that the three hydrogenase isoenzymes not only are interacting at the functional level but are also interconnected during the maturation process.
Metabolic Flux Responses to Pyruvate Kinase Knockout in
Escherichia coli
Authors: Emmerling Marcel , Dauner Michael , Ponti Aaron , Fiaux Jocelyne , Hochuli Michel , Szyperski Thomas , Wüthrich Kurt , Bailey J. E. , Sauer Uwe 
Published: July 2002

ABSTRACT

The intracellular carbon flux distribution in wild-type and pyruvate kinase-deficient
Escherichia coli
was estimated using biosynthetically directed fractional
13
C labeling experiments with [U-
13
C
6
]glucose in glucose- or ammonia-limited chemostats, two-dimensional nuclear magnetic resonance (NMR) spectroscopy of cellular amino acids, and a comprehensive isotopomer model. The general response to disruption of both pyruvate kinase isoenzymes in
E. coli
was a local flux rerouting via the combined reactions of phosphoenolpyruvate (PEP) carboxylase and malic enzyme. Responses in the pentose phosphate pathway and the tricarboxylic acid cycle were strongly dependent on the environmental conditions. In addition, high futile cycling activity via the gluconeogenic PEP carboxykinase was identified at a low dilution rate in glucose-limited chemostat culture of pyruvate kinase-deficient
E. coli
, with a turnover that is comparable to the specific glucose uptake rate. Furthermore, flux analysis in mutant cultures indicates that glucose uptake in
E. coli
is not catalyzed exclusively by the phosphotransferase system in glucose-limited cultures at a low dilution rate. Reliability of the flux estimates thus obtained was verified by statistical error analysis and by comparison to intracellular carbon flux ratios that were independently calculated from the same NMR data by metabolic flux ratio analysis.
Biofilm Formation and Dispersal under the Influence of the Global Regulator CsrA of
Escherichia coli
Authors: Jackson Debra W. , Suzuki Kazushi , Oakford Lawrence , Simecka Jerry W. , Hart Mark E. , Romeo Tony 
Published: July 2002

ABSTRACT

The predominant mode of growth of bacteria in the environment is within sessile, matrix-enclosed communities known as biofilms. Biofilms often complicate chronic and difficult-to-treat infections by protecting bacteria from the immune system, decreasing antibiotic efficacy, and dispersing planktonic cells to distant body sites. While the biology of bacterial biofilms has become a major focus of microbial research, the regulatory mechanisms of biofilm development remain poorly defined and those of dispersal are unknown. Here we establish that the RNA binding global regulatory protein CsrA (carbon storage regulator) of
Escherichia coli
K-12 serves as both a repressor of biofilm formation and an activator of biofilm dispersal under a variety of culture conditions. Ectopic expression of the
E. coli
K-12
csrA
gene repressed biofilm formation by related bacterial pathogens. A
csrA
knockout mutation enhanced biofilm formation in
E. coli
strains that were defective for extracellular, surface, or regulatory factors previously implicated in biofilm formation. In contrast, this
csrA
mutation did not affect biofilm formation by a
glgA
(glycogen synthase) knockout mutant. Complementation studies with
glg
genes provided further genetic evidence that the effects of CsrA on biofilm formation are mediated largely through the regulation of intracellular glycogen biosynthesis and catabolism. Finally, the expression of a chromosomally encoded
csrA
′
-
′
lacZ
translational fusion was dynamically regulated during biofilm formation in a pattern consistent with its role as a repressor. We propose that global regulation of central carbon flux by CsrA is an extremely important feature of
E. coli
biofilm development.