bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indole Can Act as an Extracellular Signal in
Escherichia coli
Authors: Wang Dandan , Ding Xuedong , Rather Philip N. 
Published: July 2002

ABSTRACT

Previous work has shown that
lacZ
fusions to the
cysK, astD, tnaB
, and
gabT
genes in
Escherichia coli
are activated by self-produced extracellular signals. Using a combination of ethyl acetate extraction, reversed-phase C
18
chromatography, and thin-layer chromatography, we have purified an extracellular activating signal from
E. coli
supernatants. Mass spectrometry revealed a molecule with an
m/z
peak of 117, consistent with indole. Nuclear magnetic resonance analysis of the purified
E. coli
factor and synthetic indole revealed identical profiles. Using synthetic indole, a dose-dependent activation was observed with
lacZ
fusions to the
gabT, astD
, and
tnaB
genes. However,
cysK
::
lacZ
and several control fusions were not significantly activated by indole. Conditioned medium prepared from a
tnaA
(tryptophanase) mutant, deficient in indole production, supported 26 to 41% lower activation of the
gabT
and
astD
fusions. The residual level of activation may be due to a second activating signal. Activation of the
tnaB
::
lacZ
fusion was reduced by greater than 70% in conditioned medium from a
tnaA
mutant.
Loss of
Pseudomonas aeruginosa
PhpA Aminopeptidase Activity Results in Increased
algD
Transcription
Authors: Woolwine Samuel C. , Sprinkle April B. , Wozniak Daniel J. 
Published: July 2002

ABSTRACT

Inactivation of
Pseudomonas aeruginosa phpA
, encoding a putative leucine aminopeptidase, results in increased transcription of
algD
. The homologous protein in
Escherichia coli
, PepA, is multifunctional, possessing independent aminopeptidase and DNA-binding activities. Here we provide in vitro evidence that PhpA is an aminopeptidase and show that this activity is the relevant property with regard to
algD
expression. This regulation occurred at the previously mapped
algD
transcription initiation site and was not due to activation of an alternative promoter.
Role of DnaB Helicase in UV-Induced Illegitimate Recombination in
Escherichia coli
Authors: Hanada Katsuhiro , Yamashita Teruhito , Shobuike Yuko , Ikeda Hideo 
Published: July 2002

ABSTRACT

To study the involvement of DNA replication in UV-induced illegitimate recombination, we examined the effect of temperature-sensitive
dnaB
mutations on illegitimate recombination and found that the frequency of illegitimate recombination was reduced by an elongation-deficient mutation,
dnaB14
, but not by an initiation-deficient mutation,
dnaB252
. This result indicates that DNA replication is required for UV-induced illegitimate recombination. In addition, the
dnaB14
mutation also affected spontaneous or UV-induced illegitimate recombination enhanced by the
recQ
mutation. Nucleotide sequence analyses of the recombination junctions showed that DnaB-mediated illegitimate recombination is short homology dependent. Previously, Michel et al. (B. Michel, S. Ehrlich, and M. Uzest, EMBO J. 16:430–438, 1997) showed that thermal treatment of the temperature-sensitive
dnaB8
mutant induces double-stranded breaks, implying that induction of illegitimate recombination occurs. To explain the discrepancy between the observations, we propose a model for DnaB function, in which the
dnaB
mutations may exhibit two types of responses, early and late responses, for double-stranded break formation. In the early response, replication forks stall at damaged DNA, resulting in the formation of double-stranded breaks, and the
dnaB14
mutation reduces the double-stranded breaks shortly after temperature shift-up. On the other hand, in the late response, the arrested replication forks mediated by the
dnaB8
mutation may induce double-stranded breaks after prolonged incubation.
The
Saccharomyces
cerevisiae
Isw2p-Itc1p Complex Represses
INO1
Expression and Maintains Cell Morphology
Authors: Sugiyama Minetaka , Nikawa Jun-Ichi 
Published: July 2002

ABSTRACT

In the yeast
Saccharomyces
cerevisiae
,
IRE1
encodes a bifunctional protein with transmembrane kinase and endoribonuclease activities.
HAC1
encodes a transcription factor which has a basic leucine zipper domain. Both gene products play a crucial role in the unfolded protein response. Mutants in which one of these genes is defective also show the inositol-auxotrophic (Ino
−
) phenotype, but the reason for this has not been clear. To investigate the mechanism underlying the Ino
−
phenotype, we screened a multicopy suppressor gene which can suppress the Ino
−
phenotype of the Δ
hac1
strain. We obtained a truncated form of the
ITC1
gene that has a defect in its 3′ region. Although the truncated form of
ITC1
clearly suppressed the Ino
−
phenotype of the Δ
hac1
strain, the full-length
ITC1
had a moderate effect. The gene products of
ITC1
and
ISW2
are known to constitute a chromatin-remodeling complex (T. Tsukiyama, J. Palmer, C. C. Landel, J. Shiloach, and C. Wu, Genes Dev. 13:686–697, 1999). Surprisingly, the deletion of either
ITC1
or
ISW2
in the Δ
hac1
strain circumvented the inositol requirement and caused derepression of
INO1
even under repression conditions, i.e., in inositol-containing medium. These data indicate that the Isw2p-Itc1p complex usually represses
INO1
expression and that overexpression of the truncated form of
ITC1
functions in a dominant negative manner in
INO1
repression. It is conceivable that the repressor function of this complex is regulated by the C-terminal region of Itc1p.
Identification and Characterization of a Novel 38.5-Kilodalton Cell Surface Protein of
Staphylococcus aureus
with Extended-Spectrum Binding Activity for Extracellular Matrix and Plasma Proteins
Authors: Hussain Muzaffar , Becker Karsten , von Eiff Christof , Schrenzel Jacques , Peters Georg , Herrmann Mathias 
Published: July 2002

ABSTRACT

The ability to attach to host ligands is a well-established pathogenic factor in invasive
Staphylococcus aureus
disease. In addition to the family of adhesive proteins bound to the cell wall via the sortase A (
srtA
) mechanism, secreted proteins such as the fibrinogen-binding protein Efb, the extracellular adhesion protein Eap, or coagulase have been found to interact with various extracellular host molecules. Here we describe a novel protein, the extracellular matrix protein-binding protein (Emp) initially identified in Western ligand blots as a 40-kDa protein due to its broad-spectrum recognition of fibronectin, fibrinogen, collagen, and vitronectin. Emp is expressed in the stationary growth phase and is closely associated with the cell surface and yet is extractable by sodium dodecyl sulfate. The conferring gene
emp
(1,023 nucleotides) encodes a signal peptide of 26 amino acids and a mature protein of a calculated molecular mass of 35.5 kDa. Using PCR,
emp
was demonstrated in all 240
S. aureus
isolates of a defined clinical strain collection as well as in 6
S. aureus
laboratory strains, whereas it is lacking in all 10
S. epidermidis
strains tested. Construction of an allelic replacement mutant (mEmp50) revealed the absence of Emp in mEmp50, a significantly decreased adhesion of mEmp50 to immobilized fibronectin and fibrinogen, and restoration of these characteristics upon complementation of mEmp50. Emp expression was also demonstrable upon heterologous complementation of
S. carnosus
. rEmp expressed in
Escherichia coli
interacted with fibronectin, fibrinogen, and vitronectin in surface plasmon resonance experiments at a
K

d

of 21 nM, 91 nM, and 122 pM, respectively. In conclusion, the biologic characterization of Emp suggests that it is a member of the group of secreted
S. aureus
molecules that interact with an extended spectrum of host ligands and thereby contribute to
S. aureus
pathogenicity.
Gene Transfer to the Desiccation-Tolerant Cyanobacterium
Chroococcidiopsis
Authors: Billi Daniela , Friedmann E. Imre , Helm Richard F. , Potts Malcolm 
Published: July 2002

ABSTRACT

The coccoid cyanobacterium
Chroococcidiopsis
dominates microbial communities in the most extreme arid hot and cold deserts. These communities withstand constraints that result from multiple cycles of drying and wetting and/or prolonged desiccation, through mechanisms which remain poorly understood. Here we describe the first system for genetic manipulation of
Chroococcidiopsis
. Plasmids pDUCA7 and pRL489, based on the pDU1 replicon of
Nostoc
sp. strain PCC 7524, were transferred to different isolates of
Chroococcidiopsis
via conjugation and electroporation. This report provides the first evidence that pDU1 replicons can be maintained in cyanobacteria other than
Nostoc
and
Anabaena
. Following conjugation, both plasmids replicated in
Chroococcidiopsis
sp. strains 029, 057, and 123 but not in strains 171 and 584. Both plasmids were electroporated into strains 029 and 123 but not into strains 057, 171, and 584. Expression of P

psb
A

-
luxAB
on pRL489 was visualized through in vivo luminescence. Efficiencies of conjugative transfer for pDUCA7 and pRL489 into
Chroococcidiopsis
sp. strain 029 were approximately 10
−2
and 10
−4
transconjugants per recipient cell, respectively. Conjugative transfer occurred with a lower efficiency into strains 057 and 123. Electrotransformation efficiencies of about 10
−4
electrotransformants per recipient cell were achieved with strains 029 and 123, using either pDUCA7 or pRL489. Extracellular deoxyribonucleases were associated with each of the five strains. Phylogenetic analysis, based upon the V6 to V8 variable regions of 16S rRNA, suggests that desert strains 057, 123, 171, and 029 are distinct from the type species strain
Chroococcidiopsis thermalis
PCC 7203. The high efficiency of conjugative transfer of
Chroococcidiopsis
sp. strain 029, from the Negev Desert, Israel, makes this a suitable experimental strain for genetic studies on desiccation tolerance.
Pyridoxal 5-Phosphate Inhibition of Substrate Selectivity Mutants of UhpT, the Sugar 6-Phosphate Carrier of
Escherichia coli
Authors: Hall Jason A. , Maloney Peter C. 
Published: July 2002

ABSTRACT
In the sugar phosphate transporter UhpT, gain-of-function derivatives that prefer phosphoenolpyruvate (PEP) as substrate have an uncompensated lysine residue on transmembrane segment 11. We show here that these variants are also highly susceptible to substrate-protectable inhibition by covalent modification of lysine with pyridoxal 5-phosphate. The chemical requirements of this interaction provide evidence that the gain-of-function phenotype results from the pairing of the uncompensated lysines in these mutants with the anionic carboxyl group of PEP.
Control of Butanol Formation in
Clostridium acetobutylicum
by Transcriptional Activation
Authors: Thormann Kai , Feustel Lothar , Lorenz Karin , Nakotte Stephan , Dürre Peter 
Published: July 2002

ABSTRACT

The
sol
operon of
Clostridium acetobutylicum
is the essential transcription unit for formation of the solvents butanol and acetone. The recent proposal that transcriptional regulation of this operon is controlled by the repressor Orf5/SolR (R. V. Nair, E. M. Green, D. E. Watson, G. N. Bennett, and E. T. Papoutsakis, J. Bacteriol. 181:319-330, 1999) was found to be incorrect. Instead, regulation depends on activation, most probably by the multivalent transcription factor Spo0A. The operon is transcribed from a single promoter. A second signal identified in primer extension studies results from mRNA processing and can be observed only in the natural host, not in a heterologous host. The first structural gene in the operon (
adhE
, encoding a bifunctional butyraldehyde/butanol dehydrogenase) is translated into two different proteins, the mature AdhE enzyme and the separate butanol dehydrogenase domain. The promoter of the
sol
operon is preceded by three imperfect repeats and a putative Spo0A-binding motif, which partially overlaps with repeat 3 (R3). Reporter gene analysis performed with the
lacZ
gene of
Thermoanaerobacterium thermosulfurigenes
and targeted mutations of the regulatory region revealed that the putative Spo0A-binding motif, R3, and R1 are essential for control. The data obtained also indicate that an additional activator protein is involved.
Correlation between Mutations in the Interferon Sensitivity-Determining Region of NS5A Protein and Viral Load of Hepatitis C Virus Subtypes 1b, 1c, and 2a
Authors: Lusida Maria I. , Nagano-Fujii Motoko , Nidom Chairul A. , Soetjipto  , Handajani Retno , Fujita Tsunenori , Oka Kiyomasa , Hotta Hak 
Published: July 2002

ABSTRACT

In the present study, we analyzed the possible relationship between interferon (IFN) sensitivity-determining region (ISDR) sequence variation of various hepatitis C virus (HCV) subtypes and serum HCV titers in Indonesian patients without IFN treatment. The viremia titers (mean ± standard deviation) of HCV subtype 1b (HCV-1b) isolates with low (three or fewer) and high (four or more) numbers of ISDR mutations were 5.4 ± 0.6 and 4.2 ± 0.9 log
10
RNA copies/ml, respectively, with the difference between the two groups being statistically significant (
P
< 0.01). Similarly, the viremia titers of HCV-1c isolates with low and high numbers of ISDR mutations were 5.3 ± 0.6 and <3.0 ± 0.0 log
10
RNA copies/ml, respectively, with the difference between the two groups being statistically significant (
P
< 0.01). Also, the virus titers of HCV-2a isolates with low and high numbers of ISDR mutations were 4.3 ± 0.7 and 3.5 ± 0.4 log
10
RNA copies/ml, respectively, with the difference between the two groups being statistically significant (
P
< 0.01). Thus, our results demonstrated that virus load in Indonesian patients infected with HCV-1b, HCV-1c, or HCV-2a correlated inversely with the number of mutations in the ISDR sequence, implying the possibility that the ISDR sequence plays an important role in determining the levels of HCV viremia.
Recurrent
Achromobacter piechaudii
Bacteremia in a Patient with Hematological Malignancy
Authors: Kay Stephen E. , Clark Robert A. , White Karen L. , Peel Margaret M. 
Published: July 2002

ABSTRACT

We describe a recurrent bacteremia caused by
Achromobacter
(formerly
Alcaligenes
)
piechaudii
in association with an intravenous catheter in an immunocompromised 73-year-old man. This is the first reported case of bacteremia due to
A. piechaudii
.
Detection of Rifampin-Resistant
Mycobacterium tuberculosis
in Sputa by Nested PCR-Linked Single-Strand Conformation Polymorphism and DNA Sequencing
Authors: Kim Bum-Joon , Lee Keun-Hwa , Park Bo-Na , Kim Seo-Jeong , Park Eun-Mi , Park Young-Gil , Bai Gil-Han , Kim Sang-Jae , Kook Yoon-Hoh 
Published: July 2002

ABSTRACT

Either PCR-mediated single strand conformation polymorphism (SSCP) analysis or DNA sequencing of
rpoB
DNA (157 bp) can be used as a rapid screening method for the detection of mutations related to the rifampin resistance of
Mycobacterium tuberculosis
. However, due to the nonspecific amplification of
rpoB
DNA from nontuberculous mycobacteria these methods cannot be directly applied to clinical specimens such as sputa. We developed a nested PCR method that can specifically amplify the
rpoB
DNA of
M. tuberculosis
on the basis of
rpoB
DNA sequences of 44 mycobacteria. Nested PCR-linked SSCP analysis and the DNA sequencing method were applied directly in order to detect
M. tuberculosis
and determine its rifampin susceptibility in 56 sputa. The results obtained by nested PCR-SSCP and DNA sequencing were concordant with those of conventional drug susceptibility testing and DNA sequencing performed with culture isolates.
Genetic and Phenotypic Features of
Streptococcus pyogenes
Strains Isolated in Brazil That Harbor New
emm
Sequences
Authors: Teixeira Lúcia M. , Barros Rosana R. , Castro Angela Christina D. , Peralta José Mauro , Da Glória S. Carvalho Maria , Talkington Deborah F. , Vivoni Adriana M. , Facklam Richard R. , Beall Bernard 
Published: July 2002

ABSTRACT

In the present study, 37 group A
Streptococcus
(GAS) strains belonging to 13 new
emm
sequence types identified among GAS strains randomly isolated in Brazil were characterized by using phenotypic and genotypic methods. The new types were designated
st204
,
st211
,
st213
,
st809
,
st833
,
st854
,
st2904
,
st2911
,
st2917
,
st2926
,
st3757
,
st3765
, and
st6735
. All isolates were susceptible to the antimicrobial agents tested, except to tetracycline. They all carried the
speB
gene, and 94.6% produced detectable SpeB. Most strains belonging to a given
emm
type had similar or highly related pulsed-field gel electrophoresis profiles that were distinct from profiles of strains of another type. The other characteristics were variable from isolate to isolate, although some associations were consistently found within some
emm
types. Unlike the other isolates, all type
st213
isolates were
speA
positive and produced SpeA. Strains belonging to
st3765
were T6 and opacity factor (OF) negative. Individual isolates within OF-positive
emm
types were associated with unique
sof
gene sequence types, while OF-negative isolates were
sof
negative by PCR. This report provides information on new
emm
sequence types first detected in GAS isolates from a geographic area not extensively surveyed. Such data can contribute to a better understanding of the local and global dynamics of GAS populations and of the epidemiological aspects of GAS infections occurring in tropical regions.
Competing Death Programs in Poliovirus-Infected Cells: Commitment Switch in the Middle of the Infectious Cycle
Authors: Agol Vadim I. , Belov George A. , Bienz Kurt , Egger Denise , Kolesnikova Marina S. , Romanova Lyudmila I. , Sladkova Larissa V. , Tolskaya Elena A. 
Published: July 2002

ABSTRACT
Productive poliovirus infection of HeLa cells leads to the canonical cytopathic effect (CPE), whereas certain types of abortive infection result in apoptosis. To define the time course of commitment to the different types of poliovirus-induced death, inhibitors of viral replication (guanidine HCl) or translation (cycloheximide) were added at different times postinfection (p.i.). Early in the infection (during the first ∼2 h p.i.), predominantly proapoptotic viral function was expressed, rendering the cells committed to apoptosis, which developed several hours after viral expression was arrested. In the middle of infection, concomitantly with the onset of fast generation of viral progeny, the implementation of the viral apoptotic program was abruptly interrupted. In particular, activation of an Asp-Glu-Val-Asp (DEVD)-specific caspase(s) occurring in the apoptosis-committed cells was prevented by the ongoing productive infection. Simultaneously, the cells retaining normal or nearly normal morphology became committed to CPE, which eventually developed regardless of whether or not further viral expression was allowed to proceed. The implementation of the poliovirus-induced apoptotic program was suppressed in HeLa cells overexpressing the Bcl-2 protein, indicating that the fate of poliovirus-infected cells depends on the balance of host and viral pro- and antiapoptotic factors.
Efficient Lytic Infection of Human Arterial Endothelial Cells by Human Cytomegalovirus Strains
Authors: Kahl M. , Siegel-Axel D. , Stenglein S. , G.  , Jahn  , Sinzger C. 
Published: July 2002

ABSTRACT
Endothelial cells (EC) are common targets of permissive infection by human cytomegalovirus (HCMV) in vivo during acute disease. However, studies of HCMV-EC interactions in vitro have generated discordant results. While lytic infection of cultured venous EC has been well established, Fish et al. (K. N. Fish, C. Soderberg Naucler, L. K. Mills, S. Stenglein, and J. A. Nelson, J. Virol. 72:5661–5668) have reported noncytopathic persistence of the virus in cultured aortic EC. We propose that interstrain differences in viral host cell tropism rather than the vascular bed of origin of infected EC might account for these discrepancies. In the present investigation we compared the responses of EC derived from human adult iliac artery, placental microvasculature, and umbilical vein to infection with various HCMV strains. Regardless of the vascular bed of origin, infection with EC-propagated HCMV strains induced 100% efficient cytopathic change progressing to complete lysis of inoculated monolayers. While fibroblast-propagated strains persisted at low titer in infected arterial EC cultures, they were also cytolytic for individual infected cells. The finding of cytopathic lytic infection of arterial EC by HCMV implicates a mechanism of vascular injury in the pathogenesis of HCMV infection.
The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity
Authors: Oelrichs Robert B. , Shrestha Iswar L. , Anderson David A. , Deacon Nicholas J. 
Published: July 2002

ABSTRACT
An explosive epidemic of human immunodeficiency virus type 1 (HIV-1) has been documented among the injecting drug user population of Kathmandu, Nepal, whose seropositivity rate has risen from 0 to 40% between 1995 and 1997. By using Catrimox to preserve whole-blood RNA at ambient temperature for transportation, HIV-1 envelope V3–V4 sequences were obtained from 36 patients in this group. Analysis of the sequences indicated a homogenous epidemic of subtype C virus, with at least two independent introductions of the virus into the population. Viral diversity was restricted within two transmission subclusters, with the majority of variation occurring in V4. Calculation of the synonymous-to-nonsynonymous mutation ratio (Ks:Ka) across this region showed that significant evolutionary pressure had been experienced during the rapid horizontal spread of the virus in this population, most strongly directed to the region between V3 and V4.
Incorporation of Lysyl-tRNA Synthetase into Human Immunodeficiency Virus Type 1
Authors: Cen Shan , Khorchid Ahmad , Javanbakht Hassan , Gabor Juliana , Stello Timothy , Shiba Kiyotaka , Musier-Forsyth Karin , Kleiman Lawrence 
Published: July 2002

ABSTRACT

During human immunodeficiency virus type 1 (HIV-1) assembly, tRNA
Lys
isoacceptors are selectively incorporated into virions and tRNA

3

Lys

is used as the primer for reverse transcription. We show herein that the tRNA
Lys
-binding protein, lysyl-tRNA synthetase (LysRS), is also selectively packaged into HIV-1. The viral precursor protein Pr55

gag

alone will package LysRS into Pr55

gag

particles, independently of tRNA
Lys
. With the additional presence of the viral precursor protein Pr160

gag-pol

, tRNA
Lys
and LysRS are both packaged into the particle. While the predominant cytoplasmic LysRS has an apparent
M
r
of 70,000, viral LysRS associated with tRNA
Lys
packaging is shorter, with an apparent
M
r
of 63,000. The truncation occurs independently of viral protease and might be required to facilitate interactions involved in the selective packaging and genomic placement of primer tRNA

3

Lys

.