bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of Protoanemonin from 2-Chloro-cis,cis-Muconate by the Combined Action of Muconate Cycloisomerase and Muconolactone Isomerase
Authors: Skiba Anke , Hecht Volker , Pieper Dietmar Helmut 
Published: February 2003

ABSTRACTMuconate cycloisomerases are known to catalyze the reversible conversion of 2-chloro-cis,cis-muconate by 1,4- and 3,6-cycloisomerization into (4S)-(+)-2-chloro- and (4R/5S)-(+)-5-chloromuconolactone. 2-Chloromuconolactone is transformed by muconolactone isomerase with concomitant dechlorination and decarboxylation into the antibiotic protoanemonin. The lowkcatfor this compound compared to that for 5-chloromuconolactone suggests that protoanemonin formation is of minor importance. However, since 2-chloromuconolactone is the initially predominant product of 2-chloromuconate cycloisomerization, significant amounts of protoanemonin were formed in reaction mixtures containing large amounts of muconolactone isomerase and small amounts of muconate cycloisomerase. Such enzyme ratios resemble those observed in cell extracts of benzoate-grown cells ofRalstonia eutrophaJMP134. In contrast,cis-dienelactone was the predominant product formed by enzyme preparations, in which muconolactone isomerase was in vitro rate limiting. In reaction mixtures containing chloromuconate cycloisomerase and muconolactone isomerase, only minute amounts of protoanemonin were detected, indicating that only small amounts of 2-chloromuconolactone were formed by cycloisomerization and that chloromuconate cycloisomerase actually preferentially catalyzes a 3,6-cycloisomerization.
Loss of Catabolite Repression Function of HPr, the Phosphocarrier Protein of the Bacterial Phosphotransferase System, Affects Expression of the
cry4A
Toxin Gene in
Bacillus thuringiensis
subsp.
israelensis
Authors: Khan Sharik R. , Banerjee-Bhatnagar Nirupama 
Published: February 2003

ABSTRACT

HPr, the phosphocarrier protein of the bacterial phosphotransferase system, mediates catabolite repression of a number of operons in gram-positive bacteria. In order to participate in the regulatory process, HPr is activated by phosphorylation of a conserved serine-46 residue. To study the potential role of HPr in the regulation of Cry4A protoxin synthesis in
Bacillus thuringiensis
subsp.
israelensis
, we produced a catabolite repression-negative mutant by replacing the wild-type copy of the
ptsH
gene with a mutated copy in which the conserved serine residue of HPr was replaced with an alanine. HPr isolated from the mutant strain was not phosphorylated at Ser-45 by HPr kinase, but phosphorylation at His-14 was found to occur normally. The enzyme I and HPr kinase activities of the mutant were not affected. Analysis of the
B. thuringiensis
subsp.
israelensis
mutant harboring
ptsH
-S45A in the chromosome showed that
cry4A
expression was derepressed from the inhibitory effect of glucose. The mutant strain produced both
cry4A
and σ
35
gene transcripts 4 h ahead of the parent strain, but there was no effect on σ
28
synthesis. In wild-type
B. thuringiensis
subsp.
israelensis
cells,
cry4A
mRNA was observed from 12 h onwards, while in the mutant it appeared at 8 h and was produced for a longer period. The total amount of
cry4A
transcripts produced by the mutant was higher than by the parent strain. There was a 60 to 70% reduction in the sporulation efficiency of the mutant
B. thuringiensis
subsp.
israelensis
strain compared to the wild-type strain.
Envelope Disorder of
Escherichia coli
Cells Lacking Phosphatidylglycerol
Authors: Suzuki Motoo , Hara Hiroshi , Matsumoto Kouji 
Published: February 2003

ABSTRACT

Phosphatidylglycerol, the most abundant acidic phospholipid in
Escherichia coli
, is considered to play specific roles in various cellular processes that are essential for cell viability. A null mutation of
pgsA
, which encodes phosphatidylglycerophosphate synthase, does indeed confer lethality. However,
pgsA
null mutants are viable if they lack the major outer membrane lipoprotein (Lpp) (
lpp
mutant) (S. Kikuchi, I. Shibuya, and K. Matsumoto, J. Bacteriol. 182:371-376, 2000). Here we show that Lpp expressed from a plasmid causes cell lysis in a
pgsA lpp
double mutant. The envelopes of cells harvested just before lysis could not be separated into outer and inner membrane fractions by sucrose density gradient centrifugation. In contrast, expression of a mutant Lpp (LppΔK) lacking the COOH-terminal lysine residue (required for covalent linking to peptidoglycan) did not cause lysis and allowed for the clear separation of the outer and inner membranes. We propose that in
pgsA
mutants LppΔK could not be modified by the addition of a diacylglyceryl moiety normally provided by phosphatidylglycerol and that this defect caused unmodified LppΔK to accumulate in the inner membrane. Although LppΔK accumulation did not lead to lysis, the accumulation of unmodified wild-type Lpp apparently led to the covalent linking to peptidoglycan, causing the inner membrane to be anomalously anchored to peptidoglycan and eventually leading to lysis. We suggest that this anomalous anchoring largely explains a major portion of the nonviable phenotypes of
pgsA
null mutants.
Identification of the Origin of Replication of the
Mycoplasma pulmonis
Chromosome and Its Use in
oriC
Replicative Plasmids
Authors: Cordova Caio M. M. , Lartigue Carole , Sirand-Pugnet Pascal , Renaudin Joël , Cunha Regina A. F. , Blanchard A. 
Published: February 2003

ABSTRACT

Mycoplasma pulmonis
is a natural rodent pathogen, considered a privileged model for studying respiratory mycoplasmosis. The complete genome of this bacterium, which belongs to the class
Mollicutes
, has recently been sequenced, but studying the role of specific genes requires improved genetic tools. In silico comparative analysis of sequenced mollicute genomes indicated the lack of conservation of gene order in the region containing the predicted origin of replication (
oriC
) and the existence, in most of the mollicute genomes examined, of putative DnaA boxes lying upstream and downstream from the
dnaA
gene. The predicted
M. pulmonis oriC
region was shown to be functional after cloning it into an artificial plasmid and after transformation of the mycoplasma, which was obtained with a frequency of 3 × 10
−6
transformants/CFU/μg of plasmid DNA. However, after a few in vitro passages, this plasmid integrated into the chromosomal
oriC
region. Reduction of this
oriC
region by subcloning experiments to the region either upstream or downstream from
dnaA
resulted in plasmids that failed to replicate in
M. pulmonis
, except when these two intergenic regions were cloned with the
tetM
determinant as a spacer in between them. An internal fragment of the
M. pulmonis
hemolysin A gene (
hlyA
) was cloned into this
oriC
plasmid, and the resulting construct was used to transform
M. pulmonis
. Targeted integration of this genetic element into the chromosomal
hlyA
by a single crossing over, which results in the disruption of the gene, could be documented. These mycoplasmal
oriC
plasmids may therefore become valuable tools for investigating the roles of specific genes, including those potentially implicated in pathogenesis.
A Monocarboxylate Permease of
Rhizobium leguminosarum
Is the First Member of a New Subfamily of Transporters
Authors: Hosie A. H. F. , Allaway D. , Poole P. S. 
Published: February 2003

ABSTRACT

Amino acid transport by
Rhizobium leguminosarum
is dominated by two ABC transporters, the general amino acid permease (Aap) and the branched-chain amino acid permease (Bra). However, mutation of these transporters does not prevent this organism from utilizing alanine for growth. An
R. leguminosarum
permease (MctP) has been identified which is required for optimal growth on alanine as a sole carbon and nitrogen source. Characterization of MctP confirmed that it transports alanine (

K
m

= 0.56 mM) and other monocarboxylates such as lactate and pyruvate (

K
m

= 4.4 and 3.8 μM, respectively). Uptake inhibition studies indicate that propionate, butyrate, α-hydroxybutyrate, and acetate are also transported by MctP, with the apparent affinity for solutes demonstrating a preference for C
3
-monocarboxylates. MctP has significant sequence similarity to members of the sodium/solute symporter family. However, sequence comparisons suggest that it is the first characterized permease of a new subfamily of transporters. While transport via MctP was inhibited by CCCP, it was not apparently affected by the concentration of sodium. In contrast, glutamate uptake in
R. leguminosarum
by the
Escherichia coli
GltS system did require sodium, which suggests that MctP may be proton coupled. Uncharacterized members of this new subfamily have been identified in a broad taxonomic range of species, including proteobacteria of the β-subdivision, gram-positive bacteria, and archaea. A two-component sensor-regulator (MctSR), encoded by genes adjacent to
mctP
, is required for activation of
mctP
expression.
DNA Gyrase Genes in
Mycobacterium tuberculosis
: a Single Operon Driven by Multiple Promoters
Authors: Unniraman Shyam , Chatterji Monalisa , Nagaraja Valakunja 
Published: February 2003

ABSTRACT

The two genes encoding DNA gyrase in
Mycobacterium tuberculosis
are present next to each other in the genome, with
gyrB
upstream of
gyrA
. We show that the primary transcript is dicistronic. However, in addition to the principal promoter, there are multiple weaker promoters that appear to fine-tune transcription. With these and other mycobacterial promoters, we propose consensus promoter sequences for two distinct sigma factors. In addition to this, the
gyr
genes in
M. tuberculosis
, as in other species, are subject to autoregulation, albeit with slower kinetics, probably reflecting the slower metabolism of the organism.
σBModulates Virulence Determinant Expression and Stress Resistance: Characterization of a FunctionalrsbUStrain Derived fromStaphylococcus aureus8325-4
Authors: Horsburgh Malcolm J. , Aish Joanne L. , White Ian J. , Shaw Les , Lithgow James K. , Foster Simon J. 
Published: February 2003

ABSTRACTThe accessory sigma factor σBcontrols a general stress response that is thought to be important forStaphylococcus aureussurvival and may contribute to virulence. The strain of choice for genetic studies, 8325-4, carries a small deletion inrsbU, which encodes a positive regulator of σBactivity. Consequently, to enable the role of σBin virulence to be addressed, we constructed anrsbU+derivative, SH1000, using a method that does not leave behind an antibiotic resistance marker. The phenotypic properties of SH1000 (8325-4rsbU+) were characterized and compared to those of 8325-4, thersbUmutant, parent strain. A recognition site for σBwas located in the promoter region ofkatA, the gene encoding the sole catalase ofS. aureus, by primer extension analysis. However, catalase expression and activity were similar in SH1000 (8325-4rsbU+), suggesting that this promoter may have a minor role in catalase expression under normal conditions. Restoration of σBactivity in SH1000 (8325-4rsbU+) resulted in a marked decrease in the levels of the exoproteins SspA and Hla, and this is likely to be mediated by reduced expression ofagrin this strain. By using Western blotting and asarA-lacZreporter assay, the levels of SarA were found to be similar in strains 8325-4 and SH1000 (8325-4rsbU+) andsigBmutant derivatives of these strains. This finding contrasts with previous reports that suggested that SarA expression levels are altered when they are measured transcriptionally. Inactivation ofsarAin each of these strains resulted in an expected decrease inagrexpression; however, the relative level ofagrin SH1000 (8325-4rsbU+) remained less than the relative levels in 8325-4 and thesigBmutant derivatives. We suggest that SarA is not likely to be the effector in the overall σB-mediated effect onagrexpression.
Mutational Analysis of the
Escherichia coli
PhoQ Sensor Kinase: Differences with the
Salmonella enterica
Serovar Typhimurium PhoQ Protein and in the Mechanism of Mg
2+
and Ca
2+
Sensing
Authors: Regelmann Adam G. , Lesley Joseph A. , Mott Christina , Stokes Lissette , Waldburger Carey D. 
Published: February 2003

ABSTRACT

The PhoP-PhoQ two-component system plays a role in Mg
2+
homeostasis and/or the virulence properties of a number of bacterial species. A
Salmonella enterica
serovar Typhimurium PhoQ sensor kinase mutant, in which the threonine at residue 48 in the periplasmic sensor domain is changed to an isoleucine, was shown previously to result in elevated expression of PhoP-activated genes and to affect mouse virulence, epithelial cell invasion, and sensitivity to macrophage killing. We characterized a complete set of proteins having amino acid substitutions at position 48 in the closely related
Escherichia coli
PhoQ protein. Numerous mutant proteins having amino acid substitutions with side chains of various sizes and characters displayed signaling phenotypes similar to that of the wild-type protein, indicating that interactions mediated by the wild-type threonine side chain are not required for normal protein function. Changes to amino acids with aromatic side chains had little impact on signaling in response to extracellular Mg
2+
but resulted in reduced sensitivity to extracellular Ca
2+
, suggesting that the mechanisms of signal transduction in response to these two divalent cations are different. Surprisingly, the Ile48 protein displayed a defective phenotype rather than the hyperactive phenotype seen with the
S. enterica
serovar Typhimurium protein. We also describe a mutant PhoQ protein lacking the extracellular sensor domain with a defect in the ability to activate PhoP. The defect does not appear to be due to reduced autokinase activity but rather appears to be due to an effect on the stability of the aspartyl-phosphate bond of phospho-PhoP.
Whole-Genome Comparison ofMycobacterium tuberculosisClinical and Laboratory Strains
Authors: Fleischmann R. D. , Alland D. , Eisen J. A. , Carpenter L. , White O. , Peterson J. , DeBoy R. , Dodson R. , Gwinn M. , Haft D. , Hickey E. , Kolonay J. F. , Nelson W. C. , Umayam L. A. , Ermolaeva M. , Salzberg S. L. , Delcher A. , Utterback T. , Weidman J. , Khouri H. , Gill J. , Mikula A. , Bishai W. , Jacobs, W. R. , Venter J. C. , Fraser C. M. 
Published: February 2003

ABSTRACTVirulence and immunity are poorly understood inMycobacterium tuberculosis.We sequenced the complete genome of theM. tuberculosisclinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample ofM. tuberculosisclinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms amongM. tuberculosisstrains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.
Characterization of Amino Acid Substitutions in KdpA, the K
+
-Binding and -Translocating Subunit of the KdpFABC Complex of
Escherichia coli
Authors: van der Laan Martin , Gaßel Michael , Altendorf Karlheinz 
Published: February 2003

ABSTRACT

When grown under K
+
limitation,
Escherichia coli
induces the K
+
-translocating KdpFABC complex. The stimulation of ATPase activity by NH
4
+
ions was shown for the first time. Substitutions in KdpA, which is responsible for K
+
binding and translocation, revealed that enzyme complexes KdpA:G232A and KdpA:G232S have completely lost their cation selectivity.
Chromosomal Amplification of the
Escherichia coli lipB
Region Confers High-Level Resistance to Selenolipoic Acid
Authors: Jordan Sean W. , Cronan, John E. 
Published: February 2003

ABSTRACT

One of the mutants (
slr7
mutant) of a wild-type
Escherichia coli
strain resistant to selenolipoic acid reported previously (K. E. Reed, T. W. Morris, and J. E. Cronan, Jr., Proc. Natl. Acad. Sci. USA 91:3720-3724, 1994) unexpectedly grew on minimal medium following transductional introduction of a
lipA
null mutation. We report that the
slr7
strain carries a duplication of the
lip
chromosomal region that causes the phenotype of the mutant strain.
Profiling Early Osmostress-Dependent Gene Expression in
Escherichia coli
Using DNA Macroarrays
Authors: Weber Arnim , Jung Kirsten 
Published: February 2003

ABSTRACT

DNA macroarray technology was used to monitor early transcriptional alterations of
Escherichia coli
in response to an osmotic upshift imposed by the addition of 0.4 M NaCl. Altered mRNA levels of 152 genes were detected; 45 genes showed increased expression while the expression of the remaining 107 genes was reduced. Northern blot analysis of several selected genes differing in their relative expression values confirmed the results obtained by the array technology.
FepA with Globular Domain Deletions Lacks Activity
Authors: Vakharia Hema L. , Postle Kathleen 
Published: February 2003

ABSTRACT

TonB-gated transporters have β-barrels containing an amino-terminal globular domain that occludes the interior of the barrel. Mutations in the globular domain prevent transport of ligands across the outer membrane. Surprisingly, FepA with deletions of the globular domain (amino acids 3 to 150 and 17 to 150) was previously reported to retain significant sensitivity to colicins B and D and to use ferric enterochelin, all in a TonB-dependent fashion. To further understand TonB interaction with the β-barrel, in the present study, proteins with deletions of amino acids 1 to 152, 7 to 152, 20 to 152, and 17 to 150 in
fepA
were constructed and expressed in a Δ
fepA
strain. In contrast to previous studies of
fepA
globular domain deletions, constructs in this study did not retain sensitivity to colicin B and conferred only marginal sensitivity to colicin D. Consistent with these observations, they failed to bind colicin B and detectably cross-link to TonB in vivo. To address this discrepancy, constructs were tested in other strains, one of which (RWB18-60) did support activity of the FepA globular domain deletion proteins constructed in this study. The characteristics of that strain, as well as the strain in which the ΔFhuA globular domain mutants were seen to be active, suggests the hypothesis that interprotein complementation by two individually nonfunctional proteins restores TonB-dependent activity.
The
Escherichia coli metD
Locus Encodes an ABC Transporter Which Includes Abc (MetN), YaeE (MetI), and YaeC (MetQ)
Authors: Merlin Christophe , Gardiner Gregory , Durand Sylvain , Masters Millicent 
Published: February 2003

ABSTRACT

We report that the genes
abc
,
yaeC
, and
yaeE
comprise
metD
, an
Escherichia coli
locus encoding a
dl
-methionine uptake system. MetD is an ABC transporter with Abc the ATPase, YaeE the permease, and YaeC the likely substrate binding protein. Expression of these genes is regulated by
l
-methionine and MetJ, a common repressor of the methionine regulon. We propose to rename
abc
,
yaeE
, and
yaeC
as
metN
,
metI
, and
metQ
, respectively.
Cold Shock Induction of the
cspL
Gene in
Lactobacillus plantarum
Involves Transcriptional Regulation
Authors: Derzelle Sylviane , Hallet Bernard , Ferain Thierry , Delcour Jean , Hols Pascal 
Published: February 2003

ABSTRACT

Fragments of the
cspL
promoter region were fused to the
gusA
reporter and reintroduced into
Lactobacillus plantarum
cells, either on multicopy plasmids or through single-copy chromosomal integration. β-Glucuronidase activity and primer extension data demonstrate that the
cspL
promoter is induced in response to cold shock and that multicopy constructs quench the induction of the resident
cspL
gene.
A Novel Gene That Bears a DnaJ Motif Influences Cyanobacterial Cell Division
Authors: Koksharova Olga A. , Wolk C. Peter 
Published: February 2003

ABSTRACT

Transposon Tn
5-
692 mutagenizes
Synechococcus
sp. strain PCC 7942 efficiently. The predicted product of the gene mutated in the Tn
5
-692-derived cell division mutant FTN2 has an N-terminal DnaJ domain, as have its cyanobacterial and plant orthologs.
Anabaena
sp. strain PCC 7120, when mutated in genes orthologous to
ftn2
and
ftn6
, forms akinete-like cells.
Duality of Rate Coding and Temporal Coding in Multilayered Feedforward Networks
Authors: Masuda Naoki , Aihara Kazuyuki 
Published: February 2003

Abstract
A functional role for precise spike timing has been proposed as an alternative hypothesis to rate coding. We show in this article that both the synchronous firing code and the population rate code can be used dually in a common framework of a single neural network model. Furthermore, these two coding mechanisms are bridged continuously by several modulatable model parameters, including shared connectivity, feedback strength, membrane leak rate, and neuron heterogeneity. The rates of change of these parameters are closely related to the response time and the timescale of learning.
Plato as "Architect of Science"
Authors: Zhmud Leonid 
Published: February 2003

AbstractThe figure of the cordial host of the Academy, who invited the most gifted mathematicians and cultivated pure research, whose keen intellect was able if not to solve the particular problem then at least to show the method for its solution: this figure is quite familiar to students of Greek science. But was the Academy as such a center of scientific research, and did Plato really set for mathematicians and astronomers the problems they should study and methods they should use? Our sources tell about Plato's friendship or at least acquaintance with many brilliant mathematicians of his day (Theodorus, Archytas, Theaetetus), but they were never his pupils, rather vice versa - he learned much from them and actively used this knowledge in developing his philosophy. There is no reliable evidence that Eudoxus, Menaechmus, Dinostratus, Theudius, and others, whom many scholars unite into the group of so-called "Academic mathematicians," ever were his pupils or close associates. Our analysis of the relevant passages (Eratosthenes' Platonicus, Sosigenes ap. Simplicius, Proclus' Catalogue of geometers, and Philodemus' History of the Academy, etc.) shows that the very tendency of portraying Plato as the architect of science goes back to the early Academy and is born out of interpretations of his dialogues.