bluuebunny/crossref_metadata_2025_split huggingface dataset:
Octanoyl-Homoserine Lactone Is the Cognate Signal for
Burkholderia mallei
BmaR1-BmaI1 Quorum Sensing
Authors: Duerkop Breck A. , Ulrich Ricky L. , Greenberg E. Peter 
Published: May 2007

ABSTRACT

Acyl-homoserine lactones (HSLs) serve as quorum-sensing signals for many
Proteobacteria
. Members of the LuxI family of signal generators catalyze the production of acyl-HSLs, which bind to a cognate receptor in the LuxR family of transcription factors. The obligate animal pathogen
Burkholderia mallei
produces several acyl-HSLs, and the
B. mallei
genome has four
luxR
and two
luxI
homologs, each of which has been established as a virulence factor. To begin to delineate the relevant acyl-HSL signals for
B. mallei
LuxR homologs, we analyzed the BmaR1-BmaI1 system. A comparison of acyl-HSL profiles from
B. mallei
ATCC 23344 and a
B. mallei bmaI1
mutant indicates that octanoyl-HSL synthesis is BmaI1 dependent. Furthermore, octanoyl-HSL is the predominant acyl-HSL produced by BmaI1 in recombinant
Escherichia coli
. The synthesis of soluble BmaR1 in recombinant
E. coli
requires octanoyl-HSL or decanoyl-HSL. Insoluble aggregates of BmaR1 are produced in the presence of other acyl-HSLs and in the absence of acyl-HSLs. The
bmaI1
promoter is activated by BmaR1 and octanoyl-HSL, and a 20-bp inverted repeat in the
bmaI1
promoter is required for
bmaI1
activation. Purified BmaR1 binds to this promoter region. These findings implicate octanoyl-HSL as the signal for BmaR1-BmaI1 quorum sensing and show that octanoyl-HSL and BmaR1 activate
bmaI1
transcription.
Mycobacterial Nonhomologous End Joining Mediates Mutagenic Repair of Chromosomal Double-Strand DNA Breaks
Authors: Stephanou Nicolas C. , Gao Feng , Bongiorno Paola , Ehrt Sabine , Schnappinger Dirk , Shuman Stewart , Glickman Michael S. 
Published: May 2007

ABSTRACT

Bacterial nonhomologous end joining (NHEJ) is a recently described DNA repair pathway best characterized in mycobacteria. Bacterial NHEJ proteins LigD and Ku have been analyzed biochemically, and their roles in linear plasmid repair in vivo have been verified genetically; yet the contributions of NHEJ to repair of chromosomal DNA damage are unknown. Here we use an extensive set of NHEJ- and homologous recombination (HR)-deficient
Mycobacterium smegmatis
strains to probe the importance of HR and NHEJ in repairing diverse types of chromosomal DNA damage. An
M. smegmatis
Δ
recA
Δ
ku
double mutant has no apparent growth defect in vitro. Loss of the NHEJ components Ku and LigD had no effect on sensitivity to UV radiation, methyl methanesulfonate, or quinolone antibiotics. NHEJ deficiency had no effect on sensitivity to ionizing radiation in logarithmic- or early-stationary-phase cells but was required for ionizing radiation resistance in late stationary phase in 7H9 but not LB medium. In addition, NHEJ components were required for repair of I-SceI mediated chromosomal double-strand breaks (DSBs), and in the absence of HR, the NHEJ pathway rapidly mutates the chromosomal break site. The molecular outcomes of NHEJ-mediated chromosomal DSB repair involve predominantly single-nucleotide insertions at the break site, similar to previous findings using plasmid substrates. These findings demonstrate that prokaryotic NHEJ is specifically required for DSB repair in late stationary phase and can mediate mutagenic repair of homing endonuclease-generated chromosomal DSBs.
Functional Comparison of the Two
Bacillus anthracis
Glutamate Racemases
Authors: Dodd Dylan , Reese Joseph G. , Louer Craig R. , Ballard Jimmy D. , Spies M. Ashley , Blanke Steven R. 
Published: May 2007

ABSTRACT

Glutamate racemase activity in
Bacillus anthracis
is of significant interest with respect to chemotherapeutic drug design, because
l
-glutamate stereoisomerization to
d
-glutamate is predicted to be closely associated with peptidoglycan and capsule biosynthesis, which are important for growth and virulence, respectively. In contrast to most bacteria, which harbor a single glutamate racemase gene, the genomic sequence of
B. anthracis
predicts two genes encoding glutamate racemases,
racE1
and
racE2
. To evaluate whether
racE1
and
racE2
encode functional glutamate racemases, we cloned and expressed
racE1
and
racE2
in
Escherichia coli
. Size exclusion chromatography of the two purified recombinant proteins suggested differences in their quaternary structures, as RacE1 eluted primarily as a monomer, while RacE2 demonstrated characteristics of a higher-order species. Analysis of purified recombinant RacE1 and RacE2 revealed that the two proteins catalyze the reversible stereoisomerization of
l
-glutamate and
d
-glutamate with similar, but not identical, steady-state kinetic properties. Analysis of the pH dependence of
l
-glutamate stereoisomerization suggested that RacE1 and RacE2 both possess two titratable active site residues important for catalysis. Moreover, directed mutagenesis of predicted active site residues resulted in complete attenuation of the enzymatic activities of both RacE1 and RacE2. Homology modeling of RacE1 and RacE2 revealed potential differences within the active site pocket that might affect the design of inhibitory pharmacophores. These results suggest that
racE1
and
racE2
encode functional glutamate racemases with similar, but not identical, active site features.
Generation of a Membrane Potential by
Lactococcus lactis
through Aerobic Electron Transport
Authors: Brooijmans R. J. W. , Poolman B. , Schuurman-Wolters G. K. , de Vos W. M. , Hugenholtz J. 
Published: May 2007

ABSTRACT

Lactococcus lactis
, a facultative anaerobic lactic acid bacterium, is known to have an increased growth yield when grown aerobically in the presence of heme. We have now established the presence of a functional, proton motive force-generating electron transfer chain (ETC) in
L. lactis
under these conditions. Proton motive force generation in whole cells was measured using a fluorescent probe (3′,3′-dipropylthiadicarbocyanine), which is sensitive to changes in membrane potential (Δψ). Wild-type cells, grown aerobically in the presence of heme, generated a Δψ even in the presence of the F
1
-F
o
ATPase inhibitor
N
,
N
′-dicyclohexylcarbodiimide, while a cytochrome
bd
-negative mutant strain (CydAΔ) did not. We also observed high oxygen consumption rates by membrane vesicles prepared from heme-grown cells, compared to CydAΔ cells, upon the addition of NADH. This demonstrates that NADH is an electron donor for the
L. lactis
ETC and demonstrates the presence of a membrane-bound NADH-dehydrogenase. Furthermore, we show that the functional respiratory chain is present throughout the exponential and late phases of growth.
Effect of a
recD
Mutation on DNA Damage Resistance and Transformation in
Deinococcus radiodurans
Authors: Servinsky Matthew D. , Julin Douglas A. 
Published: May 2007

ABSTRACT

The bacterium
Deinococcus radiodurans
is resistant to extremely high levels of DNA-damaging agents such as UV light, ionizing radiation, and chemicals such as hydrogen peroxide and mitomycin C. The organism is able to repair large numbers of double-strand breaks caused by ionizing radiation, in spite of the lack of the RecBCD enzyme, which is essential for double-strand DNA break repair in
Escherichia coli
and many other bacteria. The
D. radiodurans
genome sequence indicates that the organism lacks
recB
and
recC
genes, but there is a gene encoding a protein with significant similarity to the RecD protein of
E. coli
and other bacteria. We have generated
D. radiodurans
strains with a disruption or deletion of the
recD
gene. The
recD
mutants are more sensitive than wild-type cells to irradiation with gamma rays and UV light and to treatment with hydrogen peroxide, but they are not sensitive to treatment with mitomycin C and methyl methanesulfonate. The
recD
mutants also show greater efficiency of transformation by exogenous homologous DNA. These results are the first indication that the
D. radiodurans
RecD protein has a role in DNA damage repair and/or homologous recombination in the organism.
Distinct Centromere-LikeparSSites on the Two Chromosomes ofVibriospp
Authors: Yamaichi Yoshiharu , Fogel Michael A. , McLeod Sarah M. , Hui Monica P. , Waldor Matthew K. 
Published: May 2007

ABSTRACTVibrio cholerae, the cause of cholera, has two circular chromosomes. TheparABgenes on eachV. choleraechromosome act to control chromosome segregation in a replicon-specific fashion. The chromosome I (ChrI)parABgenes (parAB1) govern the localization of the origin region of ChrI, while the chromosome II (ChrII)parABgenes (parAB2) control the segregation of ChrII. In addition to ParA and ParB proteins, Par systems require ParB binding sites (parS). Here we identified theparSsites on bothV. choleraechromosomes. We found three clustered origin-proximal ParB1 bindingparS1sites on ChrI. Deletion of these threeparS1sites abrogated yellow fluorescent protein (YFP)-ParB1 focus formation in vivo and resulted in mislocalization of the ChrI origin region. However, as observed in aparA1mutant, mislocalization of the ChrI origin region in theparS1mutant did not compromiseV. choleraegrowth, suggesting that additional (non-Par-related) mechanisms may mediate the partitioning of ChrI. We also identified 10 ParB2 bindingparS2sites, which differed in sequence fromparS1. Fluorescent derivatives of ParB1 and ParB2 formed foci only with the cognateparSsequence.parABS2appears to form a functional partitioning system, as we found thatparABS2was sufficient to stabilize an ordinarily unstable plasmid inEscherichia coli. MostparS2sites were located within 70 kb of the ChrII origin of replication, but oneparS2site was found in the terminus region of ChrI. In contrast, in other sequenced vibrio species, the distribution ofparS1andparS2sites was entirely chromosome specific.
Transcriptional Regulation of the
virR
Operon of the Intracellular Pathogen
Rhodococcus equi
Authors: Byrne Gavin A. , Russell Dean A. , Chen Xiaoxiao , Meijer Wim G. 
Published: May 2007

ABSTRACT

The
virR
operon, located on the virulence plasmid of the intracellular pathogen
Rhodococcus equi
, contains five genes, two of which (
virR
and
orf8
) encode transcriptional regulators. The first gene of the operon (
virR
), encoding a LysR-type transcriptional regulator, is transcribed at a constitutive low level, whereas the four downstream genes are induced by low pH and high growth temperature. Differential regulation of the
virR
operon genes could not be explained by differential mRNA stability, as there were no major differences in mRNA half-lives of the transcripts representing each of the five genes within the
virR
operon. Transcription of
virR
is driven by the P

virR

promoter, with a transcription start site 53 bp upstream of the
virR
initiation codon. The four genes downstream of
virR
are transcribed from P

virR

and from a second promoter, P

orf5

, located 585 bp downstream of the
virR
initiation codon. VirR binds to a site overlapping the initiation codon of
virR
, resulting in negative autoregulation of the
virR
gene, explaining its low constitutive transcription level. The P

orf5

promoter is induced by high temperature and low pH, thus explaining the observed differential gene expression of the
virR
operon. VirR has a positive effect on P

orf5

activity, whereas the response regulator encoded by
orf8
is not involved in regulating transcription of the
virR
operon. The P

virR

promoter is strikingly similar to those recognized by the principal sigma factors of
Streptomyces
and
Mycobacterium
, whereas the P

orf5

promoter does not share sequence similarity with P

virR

. This suggests that P

orf5

is recognized by an alternative sigma factor.
NrdR Controls Differential Expression of the
Escherichia coli
Ribonucleotide Reductase Genes
Authors: Torrents Eduard , Grinberg Inna , Gorovitz-Harris Batia , Lundström Hanna , Borovok Ilya , Aharonowitz Yair , Sjöberg Britt-Marie , Cohen Gerald 
Published: May 2007

ABSTRACT

Escherichia coli
possesses class Ia, class Ib, and class III ribonucleotide reductases (RNR). Under standard laboratory conditions, the aerobic class Ia
nrdAB
RNR genes are well expressed, whereas the aerobic class Ib
nrdEF
RNR genes are poorly expressed. The class III RNR is normally expressed under microaerophilic and anaerobic conditions. In this paper, we show that the
E. coli
YbaD protein differentially regulates the expression of the three sets of genes. YbaD is a homolog of the
Streptomyces
NrdR protein. It is not essential for growth and has been renamed NrdR. Previously,
Streptomyces
NrdR was shown to transcriptionally regulate RNR genes by binding to specific 16-bp sequence motifs, NrdR boxes, located in the regulatory regions of its RNR operons. All three
E. coli
RNR operons contain two such NrdR box motifs positioned in their regulatory regions. The NrdR boxes are located near to or overlap with the promoter elements. DNA binding experiments showed that NrdR binds to each of the upstream regulatory regions. We constructed deletions in
nrdR
(
ybaD
) and showed that they caused high-level induction of transcription of the class Ib RNR genes but had a much smaller effect on induction of transcription of the class Ia and class III RNR genes. We propose a model for differential regulation of the RNR genes based on binding of NrdR to the regulatory regions. The model assumes that differences in the positions of the NrdR binding sites, and in the sequences of the motifs themselves, determine the extent to which NrdR represses the transcription of each RNR operon.
CcpA-Dependent and -Independent Control of Beta-Galactosidase Expression in
Streptococcus pneumoniae
Occurs via Regulation of an Upstream Phosphotransferase System-Encoding Operon
Authors: Kaufman Greer E. , Yother Janet 
Published: May 2007

ABSTRACT

A spontaneous mutant of
Streptococcus pneumoniae
strain D39 exhibiting elevated β-galactosidase activity was identified. We determined that the β-galactosidase activity was due to BgaA, a surface protein in
S. pneumoniae
, and that the expression of
bgaA
was regulated. Transcription analyses demonstrated expression of
bgaA
in the constitutive β-galactosidase (BgaA
C
) mutant, but not in the parent. β-Galactosidase expression was induced in the parent under specific growth conditions; however, the levels did not reach those of the BgaA
C
mutant. We localized the mutation resulting in the BgaA
C
phenotype to a region upstream of
bgaA
and in the promoter of a phosphoenolpyruvate-dependent phosphotransferase system (PTS) operon. The mutation was in a catabolite-responsive element (
cre
) and affected the binding of CcpA (catabolite control protein A), a key regulator of many carbon metabolism genes. The
pts
operon and
bgaA
were cotranscribed, and their transcription was regulated by CcpA. Deletion of
ccpA
altered β-galactosidase activity, leading to a sevenfold increase in the parent but a fivefold decrease in the BgaA
C
mutant. The resulting β-galactosidase activities were the same in the two strains, suggesting the presence of a second repressor. The presence of glucose in the growth medium resulted in
pts-bgaA
repression by both CcpA and the second repressor, with the latter being important in responding to the glucose concentration. Expression of β-galactosidase is important for
S. pneumoniae
adherence during colonization of the nasopharynx, a site normally devoid of glucose. CcpA and environmental glucose concentrations thus appear to play important roles in the regulation of a niche-specific virulence factor.
Identification of Regions Critically Affecting Kinetics and Allosteric Regulation of theEscherichia coliADP-Glucose Pyrophosphorylase by Modeling and Pentapeptide-Scanning Mutagenesis
Authors: Ballicora Miguel A. , Erben Esteban D. , Yazaki Terutaka , Bertolo Ana L. , Demonte Ana M. , Schmidt Jennifer R. , Aleanzi Mabel , Bejar Clarisa M. , Figueroa Carlos M. , Fusari Corina M. , Iglesias Alberto A. , Preiss Jack 
Published: May 2007

ABSTRACTADP-glucose pyrophosphorylase (ADP-Glc PPase) is the enzyme responsible for the regulation of bacterial glycogen synthesis. To perform a structure-function relationship study of theEscherichia coliADP-Glc PPase enzyme, we studied the effects of pentapeptide insertions at different positions in the enzyme and analyzed the results with a homology model. We randomly inserted 15 bp in a plasmid with the ADP-Glc PPase gene. We obtained 140 modified plasmids with single insertions of which 21 were in the coding region of the enzyme. Fourteen of them generated insertions of five amino acids, whereas the other seven created a stop codon and produced truncations. Correlation of ADP-Glc PPase activity to these modifications validated the enzyme model. Six of the insertions and one truncation produced enzymes with sufficient activity for theE. colicells to synthesize glycogen and stain in the presence of iodine vapor. These were in regions away from the substrate site, whereas the mutants that did not stain had alterations in critical areas of the protein. The enzyme with a pentapeptide insertion between Leu102and Pro103was catalytically competent but insensitive to activation. We postulate this region as critical for the allosteric regulation of the enzyme, participating in the communication between the catalytic and regulatory domains.
Adaptor Function of PapF Depends on Donor Strand Exchange in P-Pilus Biogenesis of
Escherichia coli
Authors: Lee Yvonne M. , Dodson Karen W. , Hultgren Scott J. 
Published: May 2007

ABSTRACT
P-pilus biogenesis occurs via the highly conserved chaperone-usher pathway and involves the strict coordination of multiple subunit proteins. All nonadhesin structural P-pilus subunits possess the same topology, consisting of two domains: an incomplete immunoglobulin-like fold (pilin body) and an N-terminal extension. Pilus subunits form interactions with one another through donor strand exchange, occurring at the usher, in which the N-terminal extension of an incoming subunit completes the pilin body of the preceding subunit, allowing the incorporation of the subunit into the pilus fiber. In this study, pilus subunits in which the N-terminal extension was either deleted or swapped with that of another subunit were used to examine the role of each domain of PapF in functions involving donor strand exchange and hierarchical assembly. We found that the N-terminal extension of PapF is required to adapt the PapG adhesin to the tip of the fiber. The pilin body of PapF is required to efficiently initiate assembly of the remainder of the pilus, with the assistance of the N-terminal extension. Thus, distinct functions were assigned to each region of the PapF subunit. In conclusion, all pilin subunits possess the same overall architectural topology; however, each N-terminal extension and pilin body has specific functions in pilus biogenesis.
Vibrio cholerae
Strains Possess Multiple Strategies for Abiotic and Biotic Surface Colonization
Authors: Mueller Ryan S. , McDougald Diane , Cusumano Danielle , Sodhi Nidhi , Kjelleberg Staffan , Azam Farooq , Bartlett Douglas H. 
Published: May 2007

ABSTRACT

Despite its notoriety as a human pathogen,
Vibrio cholerae
is an aquatic microbe suited to live in freshwater, estuarine, and marine environments where biofilm formation may provide a selective advantage. Here we report characterization of biofilms formed on abiotic and biotic surfaces by two non-O1/O139
V. cholerae
strains, TP and SIO, and by the O1
V. cholerae
strain N16961 in addition to the isolation of 44 transposon mutants of SIO and TP impaired in biofilm formation. During the course of characterizing the mutants, 30 loci which have not previously been associated with
V. cholerae
biofilms were identified. These loci code for proteins which perform a wide variety of functions, including amino acid metabolism, ion transport, and gene regulation. Also, when the plankton colonization abilities of strains N16961, SIO, and TP were examined, each strain showed increased colonization of dead plankton compared with colonization of live plankton (the dinoflagellate
Lingulodinium polyedrum
and the copepod
Tigriopus californicus
). Surprisingly, most of the biofilm mutants were not impaired in plankton colonization. Only mutants impaired in motility or chemotaxis showed reduced colonization. These results indicate the presence of both conserved and variable genes which influence the surface colonization properties of different
V. cholerae
subspecies.
Effects of experience in a dynamic environment on postural control
Authors: Chapman D W , Needham K J , Allison G T , Lay B , Edwards D J 
Published: May 2007

Background:Surfing is a balance-reliant, open skill performed in a dynamic environment rich in visual, somatosensory and vestibular information.Objective:To evaluate adaptations to the postural control system by surfing experience.Methods:Postural control was assessed in an upright bipedal stance in 60 male volunteers (21 elite surfers, 20 intermediate level surfers, and 19 controls) using various closed-stance positions. Six tasks were performed with two trials including a cognitive task, in the following order: eyes open, head in a neutral position (EO1); eyes closed, head in a neutral position (EC); eyes closed, head back (ECHB); eyes open, head in a neutral position, cognitive task 1 (EOC1); eyes open head in a neutral position, cognitive task 2 (EOC2); eyes open head in a neutral position (EO2). Dependent variables were area of 95th centile ellipse (AoE) and sway path length (SPL).Results:All participants showed systematic increases in SPL and AoE in EC and ECHB trials. Expert surfers displayed significantly (p<0.05) increased SPL but not AoE when sharing attention with both concurrent mental tasks compared with controls. Controls showed a slight, non-significant change in postural control (reduced SPL and AoE) when attending to concurrent mental tasks.Conclusions:The findings indicate that standard postural sway indices are not able to elucidate whether expertise in surfing facilitates adaptations to the postural control system. However, concurrent mental task findings illustrate that systematic differences in balance abilities between expert surfers and controls may exist.
Exercise pretraining protects against cerebral ischaemia induced by heat stroke in rats
Authors: Chen Yu-Wen , Chen Sheng-Hsien , Chou Willy , Lo Yi-Ming , Hung Ching-Hsia , Lin Mao-Tsun 
Published: May 2007

Background:In the rat brain, heat-stroke-induced damage to cerebral neurons is attenuated through heat-shock-induced overexpression of heat-shock protein 72 (HSP72).Objective:To ascertain whether progressive exercise preconditioning induces HSP72 expression in the rat brain and prevents heat-stroke-induced cerebral ischaemia and injury.Methods:Male Wistar rats were randomly assigned to either a sedentary group or an exercise group. Those in the exercise group progressively ran on a treadmill 5 days/week, for 30–60 min/day at an intensity of 20–30 m/min for 3 weeks. The effects of heat stroke on mean arterial pressure, cerebral blood flow, brain ischaemia markers (glutamate, lactate/pyruvate ratio and nitric oxide), a cerebral injury marker (glycerol) and brain neuronal damage score in the preconditioned animals were compared with effects in unexercised controls. Heat stroke was induced by exposing urethane-anaesthetised animals to a temperature of 43°C for 55 min, which caused the body temperature to reach 42°C.Results:Three weeks of progressive exercise pretreatment induced HSP72 preconditioning in the brain and conferred significant protection against heat-stroke-induced hyperthermia, arterial hypotension, cerebral ischaemia and neuronal damage; it also prolonged survival.Conclusions:Exercise for 3 weeks can improve heat tolerance as well as attenuate heat-stroke-induced cerebral ischaemia in rats. The maintenance of mean arterial pressure and cerebral blood flow at appropriate levels in the rat brain may be related to overexpression of HSP72.