bluuebunny/crossref_metadata_2025 huggingface dataset:
Interdependent Expression of the
ccoNOQP
-
rdxBHIS
Loci in
Rhodobacter sphaeroides
2.4.1
Authors: Roh Jung Hyeob , Kaplan Samuel
Published: February 2003

The
rdxBHIS
gene cluster of
Rhodobacter sphaeroides
2.4.1, located downstream of the
ccoNOQP
operon encoding the
cbb
3
cytochrome
c
oxidase, is required for the posttranscriptional modification of the
cbb
3
cytochrome
c
oxidase. The
cbb
3
cytochrome
c
oxidase is the main terminal oxidase under microaerobic conditions, as well as a component of the signal transduction pathway controlling photosynthesis gene expression. Because of the intimate functional and positional relationships of the
ccoNOQP
operon and the
rdxBHIS
gene cluster, we have examined the transcriptional activities of this DNA region in order to understand their expression and regulation. Northern blot analysis and reverse transcription-PCR, together with earlier complementation analysis, suggested that the
ccoNOQP
-
rdxBHIS
cluster is transcribed as
ccoNOQP
-,
ccoNOQP
-
rdxBH
-,
rdxBH
-, and
rdxIS
-specific transcripts. Multiple transcriptional start sites have been identified by primer extension analyses: five for
ccoN
, four for
rdxB
, and one for
rdxI
. Transcription from P1
N
of
ccoN
and P1
B
of
rdxB
is dependent on the presence of FnrL. LacZ fusion analysis support the above-described studies, especially the importance of FnrL. Expression of the
cco
-
rdx
cluster is closely related to photosynthesis gene expression, suggesting that transcript stoichiometry and presumably the stoichiometry of the gene products are critical factors in controlling photosynthesis gene expression.
Stimulation of Menaquinone-Dependent Electron Transfer in the Respiratory Chain ofBacillus subtilisby Membrane Energization
Authors: Azarkina N. , Konstantinov A. A.
Published: February 2003

At a pH of ≤7, respiration ofBacillus subtiliscells on endogenous substrates shut down almost completely upon addition of an uncoupler (carbonyl cyanidem-chlorophenylhydrazone [CCCP]) and a K+-ionophore (valinomycin). The same effect was observed with cell spheroplasts lacking the cell wall. The concentration of CCCP required for 50% inhibition of the endogenous respiration in the presence of K+-valinomycin was below 100 nM. Either CCCP or valinomycin alone was much less efficient than the combination of the two. The inhibitory effect was easily reversible and depended specifically on the H+and K+concentrations in the medium. Similar inhibition was observed with respect to the reduction of the artificial electron acceptors 2,6-dichlorophenolindophenol (DCPIP) andN,N,N′,N′-tetramethyl-p-phenylenediamine cation (TMPD+), which intercept reducing equivalents at the level of menaquinol. Oxidation of the reduced DCPIP or TMPD in the bacterial cells was not sensitive to uncoupling. The same loss of the electron transfer activities as induced by the uncoupling was observed upon disruption of the cells during isolation of the membranes; the residual activities were not further inhibited by the uncoupler and ionophores. We conclude that the menaquinone-dependent electron transfer in theB. subtilisrespiratory chain is facilitated, thermodynamically or kinetically, by membrane energization. A requirement for an energized state of the membrane is not a specific feature of succinate oxidation, as proposed in the literature, since it was also observed in a mutant ofB. subtilislacking succinate:quinone reductase as well as for substrates other than succinate. Possible mechanisms of the energy-dependent regulation of menaquinone-dependent respiration inB. subtilisare discussed.
Three Modifications in the D and T Arms of tRNA Influence Translation in
Escherichia coli
and Expression of Virulence Genes in
Shigella flexneri
Authors: Urbonavičius Jaunius , Durand Jérôme M. B. , Björk Glenn R.
Published: February 2003

The modified nucleosides 2′-
O
-methylguanosine, present at position 18 (Gm18), 5-methyluridine, present at position 54 (m
5
U54), and pseudouridine, present at position 55 (Ψ55), are located in the D and T arms of tRNAs and are close in space in the three-dimensional (3D) structure of this molecule in the bacterium
Escherichia coli
. The formation of these modified nucleosides is catalyzed by the products of genes
trmH
(Gm18),
trmA
(m
5
U54), and
truB
(Ψ55). The combination of
trmH
,
trmA
, and
truB
mutations resulting in lack of these three modifications reduced the growth rate, especially at high temperature. Moreover, the lack of three modified nucleotides in tRNA induced defects in the translation of certain codons, sensitivity to amino acid analog 3,4-dehydro-
dl
-proline, and an altered oxidation of some carbon compounds. The results are consistent with the suggestion that these modified nucleosides, two of which directly interact in the 3D structure of tRNA by forming a hydrogen bond between Ψ55 and Gm18, stabilize the structure of the tRNA. Moreover, lack of Ψ55 in tRNA of human pathogen
Shigella flexneri
leads to a reduced expression of several virulence-associated genes.
Activation of the
glnA
,
glnK
, and
nac
Promoters as
Escherichia coli
Undergoes the Transition from Nitrogen Excess Growth to Nitrogen Starvation
Authors: Atkinson Mariette R. , Blauwkamp Timothy A. , Bondarenko Vladamir , Studitsky Vasily , Ninfa Alexander J.
Published: February 2003

The nitrogen-regulated genes and operons of the Ntr regulon of
Escherichia coli
are activated by the enhancer-binding transcriptional activator NRI∼P (NtrC∼P). Here, we examined the activation of the
glnA
,
glnK
, and
nac
promoters as cells undergo the transition from growth on ammonia to nitrogen starvation and examined the amplification of NRI during this transition. The results indicate that the concentration of NRI is increased as cells become starved for ammonia, concurrent with the activation of Ntr genes that have less- efficient enhancers than does
glnA
. A diauxic growth pattern was obtained when
E. coli
was grown on a low concentration of ammonia in combination with arginine as a nitrogen source, consistent with the hypothesis that Ntr genes other than
glnA
become activated only upon amplification of the NRI concentration.
Context-Dependent Functions of the PII and GlnK Signal Transduction Proteins in
Escherichia coli
Authors: Atkinson Mariette R. , Blauwkamp Timothy A. , Ninfa Alexander J.
Published: February 2003

Two closely related signal transduction proteins, PII and GlnK, have distinct physiological roles in the regulation of nitrogen assimilation. Here, we examined the physiological roles of PII and GlnK when these proteins were expressed from various regulated or constitutive promoters. The results indicate that the distinct functions of PII and GlnK were correlated with the timing of expression and levels of accumulation of the two proteins. GlnK was functionally converted into PII when its expression was rendered constitutive and at the appropriate level, while PII was functionally converted into GlnK by engineering its expression from the nitrogen-regulated
glnK
promoter. Also, the physiological roles of both proteins were altered by engineering their expression from the nitrogen-regulated
glnA
promoter. We hypothesize that the use of two functionally identical PII-like proteins, which have distinct patterns of expression, may allow fine control of Ntr genes over a wide range of environmental conditions. In addition, we describe results suggesting that an additional, unknown mechanism may control the cellular level of GlnK.
Purification, Substrate Range, and Metal Center of AtzC: the
N
-Isopropylammelide Aminohydrolase Involved in Bacterial Atrazine Metabolism
Authors: Shapir Nir , Osborne Jeffrey P. , Johnson Gilbert , Sadowsky Michael J. , Wackett Lawrence P.
Published: February 2003

N
-Isopropylammelide isopropylaminohydrolase, AtzC, the third enzyme in the atrazine degradation pathway in
Pseudomonas
sp. strain ADP, catalyzes the stoichiometric hydrolysis of
N
-isopropylammelide to cyanuric acid and isopropylamine. The
atzC
gene was cloned downstream of the
tac
promoter and expressed in
Escherichia coli
, where the expressed enzyme comprised 36% of the soluble protein. AtzC was purified to homogeneity by ammonium sulfate precipitation and phenyl column chromatography. It has a subunit size of 44,938 kDa and a holoenzyme molecular weight of 174,000. The

K
m

and
k
cat
values for AtzC with
N
-isopropylammelide were 406 μM and 13.3 s
−1
, respectively. AtzC hydrolyzed other
N
-substituted amino dihydroxy-
s
-triazines, and those with linear
N
-alkyl groups had higher
k
cat
values than those with branched alkyl groups. Native AtzC contained 0.50 eq of Zn per subunit. The activity of metal-depleted AtzC was restored with Zn(II), Fe(II), Mn(II), Co(II), and Ni(II) salts. Cobalt-substituted AtzC had a visible absorbance band at 540 nm (Δε = 84 M
−1
cm
−1
) and exhibited an axial electron paramagnetic resonance (EPR) signal with the following effective values:
g

(
x
)

= 5.18,
g

(
y
)

= 3.93, and
g

(
z
)

= 2.24. Incubating cobalt-AtzC with the competitive inhibitor 5-azacytosine altered the effective EPR signal values to
g

(
x
)

= 5.11,
g

(
y
)

= 4.02, and
g

(
z
)

= 2.25 and increased the microwave power at half saturation at 10 K from 31 to 103 mW. Under the growth conditions examined, our data suggest that AtzC has a catalytically essential, five-coordinate Zn(II) metal center in the active site and specifically catalyzes the hydrolysis of intermediates generated during the metabolism of
s
-triazine herbicides.
Control of Inducer Accumulation Plays a Key Role in Succinate-Mediated Catabolite Repression in
Sinorhizobium
meliloti
Authors: Bringhurst Ryan M. , Gage Daniel J.
Published: February 2003

The symbiotic, nitrogen-fixing bacterium
Sinorhizobium
meliloti
favors succinate and related dicarboxylic acids as carbon sources. As a preferred carbon source, succinate can exert catabolite repression upon genes needed for the utilization of many secondary carbon sources, including the α-galactosides raffinose and stachyose. We isolated
lacR
mutants in a genetic screen designed to find
S
.
meliloti
mutants that had abnormal succinate-mediated catabolite repression of the
melA-agp
genes, which are required for the utilization of raffinose and other α-galactosides. The loss of catabolite repression in
lacR
mutants was seen in cells grown in minimal medium containing succinate and raffinose and grown in succinate and lactose. For succinate and lactose, the loss of catabolite repression could be attributed to the constitutive expression of β-galactoside utilization genes in
lacR
mutants. However, the inactivation of
lacR
did not cause the constitutive expression of α-galactoside utilization genes but caused the aberrant expression of these genes only when succinate was present. To explain the loss of diauxie in succinate and raffinose, we propose a model in which
lacR
mutants overproduce β-galactoside transporters, thereby overwhelming the inducer exclusion mechanisms of succinate-mediated catabolite repression. Thus, some raffinose could be transported by the overproduced β-galactoside transporters and cause the induction of α-galactoside utilization genes in the presence of both succinate and raffinose. This model is supported by the restoration of diauxie in a
lacF
lacR
double mutant (
lacF
encodes a β-galactoside transport protein) grown in medium containing succinate and raffinose. Biochemical support for the idea that succinate-mediated repression operates by preventing inducer accumulation also comes from uptake assays, which showed that cells grown in raffinose and exposed to succinate have a decreased rate of raffinose transport compared to control cells not exposed to succinate.
Forespore Signaling Is Necessary for Pro-σKProcessing duringBacillus subtilisSporulation Despite the Loss of SpoIVFA upon Translational Arrest
Authors: Kroos Lee , Yu Yuen-Tsu Nicco , Mills Denise , Ferguson-Miller Shelagh
Published: February 2003

The σKcheckpoint coordinates gene expression in the mother cell with signaling from the forespore duringBacillus subtilissporulation. The signaling pathway involves SpoIVB, a serine peptidase produced in the forespore, which is believed to cross the innermost membrane surrounding the forespore and activate a complex of proteins, including BofA, SpoIVFA, and SpoIVFB, located in the outermost membrane surrounding the forespore. Activation of the complex allows proteolytic processing of pro-σK, and the resulting σKRNA polymerase transcribes genes in the mother cell. To investigate activation of the pro-σKprocessing complex, the level of SpoIVFA in extracts of sporulating cells was examined by Western blot analysis. The SpoIVFA level decreased when pro-σKprocessing began during sporulation. In extracts of aspoIVBmutant defective in forespore signaling, the SpoIVFA level failed to decrease normally and no processing of pro-σKwas observed. Although these results are consistent with a model in which SpoIVFA inhibits processing until the SpoIVB-mediated signal is received from the forespore, we discovered that loss of SpoIVFA was insufficient to allow processing under certain conditions, including static incubation of the culture and continued shaking after the addition of inhibitors of oxidative phosphorylation or translation. Under these conditions, loss of SpoIVFA was independent ofspoIVB. The inability to process pro-σKunder these conditions was not due to loss of SpoIVFB, the putative processing enzyme, or to a requirement for ongoing synthesis of pro-σK. Rather, it was found that the requirements for shaking of the culture, for oxidative phosphorylation, and for translation could be bypassed by mutations that uncouple processing from dependence on forespore signaling. This suggests that ongoing translation is normally required for efficient pro-σKprocessing because synthesis of the SpoIVB signal protein is needed to activate the processing complex. When translation is blocked, synthesis of SpoIVB ceases, and the processing complex remains inactive despite the loss of SpoIVFA. Taken together, the results suggest that SpoIVB signaling activates the processing complex by performing another function in addition to causing loss of SpoIVFA or by causing loss of SpoIVFA in a different way than when translation is blocked. The results also demonstrate that the processing machinery can function in the absence of translation or an electrochemical gradient across membranes.
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

Muconate 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

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

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

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

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

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

The 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

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

Virulence 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

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

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

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

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

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

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

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.
CERENKOV'S EFFECT AND NEUTRINO OSCILLATIONS IN LOOP QUANTUM GRAVITY
Authors: LAMBIASE G.
Published: February 2003

Bounds on the scale parameter ℒ arising in loop quantum gravity theory are derived in the framework of Cerenkov's effect and neutrino oscillations. Assuming that ℒ is an universal constant, we infer ℒ ≳ 10-18 eV -1, a bound compatible with those inferred in different physical context.
SYMMETRY DETECTION BY RANDOM SAMPLING AND VOTING PROCESS FOR MOTION ANALYSIS
Authors: IMIYA ATSUSHI , UENO TOMOKI , FERMIN IRIS
Published: February 2003

Symmetry of an object on a plane and in a space is an important geometric feature for biology, chemistry, and the understanding of human perception of figures. We propose a randomized method for the detection of symmetry in planar polygons and polyhedrons without assuming the predetermination of the centroids of the objects. Using a voting process, which is the main concept of the Hough transform in image processing, we transform the geometric computation for symmetry detection which is usually based on graph theory and combinatorial optimization, to the peak detection problem in a voting space in the context of the Hough transform. Our algorithm detects the centroid after detecting symmetry of an object for both planar and spatial objects.
GENETIC ALGORITHM OPTIMIZATION OF ADAPTIVE MULTI-SCALE GLCM FEATURES
Authors: WALKER ROSS F. , JACKWAY PAUL T. , LONGSTAFF DENNIS
Published: February 2003

We introduce a new second-order method of texture analysis called Adaptive Multi-Scale Grey Level Co-occurrence Matrix (AMSGLCM), based on the well-known Grey Level Co-occurrence Matrix (GLCM) method. The method deviates significantly from GLCM in that features are extracted, not via a fixed 2D weighting function of co-occurrence matrix elements, but by a variable summation of matrix elements in 3D localized neighborhoods. We subsequently present a new methodology for extracting optimized, highly discriminant features from these localized areas using adaptive Gaussian weighting functions. Genetic Algorithm (GA) optimization is used to produce a set of features whose classification "worth" is evaluated by discriminatory power and feature correlation considerations. We critically appraised the performance of our method and GLCM in pairwise classification of images from visually similar texture classes, captured from Markov Random Field (MRF) synthesized, natural, and biological origins. In these cross-validated classification trials, our method demonstrated significant benefits over GLCM, including increased feature discriminatory power, automatic feature adaptability, and significantly improved classification performance.
REAL-TIME ROUTE PLANNING FOR UNMANNED AIR VEHICLE WITH AN EVOLUTIONARY ALGORITHM
Authors: ZHENG CHANGWEN , DING MINGYUE , ZHOU CHENGPING
Published: February 2003

Based on evolutionary computation, a new 3D route planner for unmanned air vehicles is presented. In our evolutionary route planner, the individual candidates are evaluated with respect to the workspace. Therefore a computation of the configuration space is avoided. With Digital Terrain Elevation Data, our approach can find a near-optimal route that can increase the surviving probability efficiently. By using a problem-specific representation of candidate solutions and genetic operators, the routes are generated in real-time and are able to take into account different kinds of mission constraints such as minimum route leg length and flying altitude, maximum turning angle, and fixed approach vector to goal position, etc.
DETECTION OF TRACKS IN AERIAL PHOTOS BY THE GIBBS SAMPLER
Authors: TETERUKOVSKIY A.
Published: February 2003

A problem of automatic detection of tracks in aerial photos is considered. We adopt a Bayesian approach and base our inference on an a priori knowledge of the structure of tracks. The probability of a pixel to belong to a track depends on how the pixel gray level differs from the gray levels of pixels in the neighborhood and on additional prior information. Several suggestions on how to formalize the prior knowledge about the shape of the tracks are made. The Gibbs sampler is used to construct the most probable configuration of tracks in the area. The method is applied to aerial photos with cell size of 1 sq. m. Even for detection of trails of width comparable with or smaller than the cell size, positive results can be achieved.
FEATURE EXTRACTION OF RADAR MULTIPLE-TARGET ECHOES USING WAVELET PACKET TRANSFORM WITH THE BEST BASES
Authors: WANG SHOUYONG , ZHU GUANGXI , TANG YUAN Y.
Published: February 2003

Extraction of effective features plays a key role in pattern recognition. A large number of patterns, such as speech, radar signals, earthquake signals, handwriting, etc. are of non-stationary signals or exhibit time-varying behavior. The features of these patterns are often located in both the time and frequency domains. The traditional methods fail to extract such kind of features. Fortunately, wavelet packet transform (WPT) can provide an arbitrary time-frequency decomposition for the signals, because a wavelet packet (WP) library contains many WP bases, which can handle the different components of a signal. Therefore, by selecting a suitable basis, which is called "best basis", the effective features can be extracted. In this paper, three criteria are used to select the best WPT basis, namely: (1) distance criterion, (2) divergence criterion and (3) entropy criterion. Three algorithms to implement the above criteria are also provided. Experiments are conducted and the positive results are obtained.
AN EFFICIENT HUMAN FACE RECOGNITION SYSTEM USING PSEUDO ZERNIKE MOMENT INVARIANT AND RADIAL BASIS FUNCTION NEURAL NETWORK
Authors: HADDADNIA JAVAD , FAEZ KARIM , AHMADI MAJID
Published: February 2003

This paper introduces a novel method for the recognition of human faces in two-dimensional digital images using a new feature extraction method and Radial Basis Function (RBF) neural network with a Hybrid Learning Algorithm (HLA) as classifier. The proposed feature extraction method includes human face localization derived from the shape information using a proposed distance measure as Facial Candidate Threshold (FCT) as well as Pseudo Zernike Moment Invariant (PZMI) with a newly defined parameter named Correct Information Ratio (CIR) of images for disregarding irrelevant information of face images. In this paper, the effect of these parameters in disregarding irrelevant information in recognition rate improvement is studied. Also we evaluate the effect of orders of PZMI in recognition rate of the proposed technique as well as learning speed. Simulation results on the face database of Olivetti Research Laboratory (ORL) indicate that high order PZMI together with the derived face localization technique for extraction of feature data yielded a recognition rate of 99.3%.
IMAGE RESTORATION: THE WAVELET-BASED APPROACH
Authors: NDJOUNTCHE TERTULIEN , UNBEHAUEN ROLF
Published: February 2003

Wavelet-based techniques are suitable for recovering a signal corrupted by noise. The time- and frequency-localization capabilities of wavelets provide better noise reduction and less signal distortion than conventional filtering methods. The noise reduction technique used in this paper is based on the hidden Markov model (HMM) structure, which can efficiently shape the statistical characteristics of practical data. As confirmed by numerical results, the HMM based approach provides a significant performance improvement over competing methods.
NON-SPHERICAL COLLAPSE OF A RADIATING STAR
Authors: GHOSH S. G. , DESHKAR D. W.
Published: February 2003

We study the junction conditions for non-spherical (plane symmetric) collapsing radiating star consisting of a shearing fluid undergoing radial heat flow with outgoing radiation. Radiation of the system is described by plane symmetric Vaidya solution. Physical quantities relating to the local conservation of momentum and surface red-shift are also obtained.
ORCHESTRATING SPATIAL REUSE IN WIRELESS AD HOC NETWORKS USING SYNCHRONOUS COLLISION RESOLUTION (SCR)
Authors: STINE JOHN A. , DE VECIANA GUSTAVO , GRACE KEVIN H. , DURST ROBERT C.
Published: February 2003

We propose a novel medium access control protocol for ad hoc wireless networks data to send can contend simultaneously for the channel. Nodes contend for access using a synchronous signaling mechanism that achieves two objectives: it arbitrates contentions locally and it selects a subset of nodes across the network that attempt to transmit simultaneously. The subset of nodes that survive the signaling mechanism can be viewed as an orchestrated set of transmissions that are spatially reusing the channel shared by the nodes. Thus the 'quality' of the subset of nodes selected by the signaling mechanism is a key factor in determining the spatial capacity of the system. In this paper, we propose a general model for such synchronous signaling mechanisms and recommend a preferred design. We then focus via both analysis and simulation on the spatial and capacity characteristics of these access control mechanisms. Our work is unique in that it specifically focuses on the spatial capacity aspects of a MAC protocol, as would be critical for ad hoc networking, and shows SCR is a promising solution. Specifically, it does not suffer from congestion collapse as the density of contending nodes grows, it does not suffer from hidden or exposed node effects, it achieves high capacities with a spatial usage exceeding 1 (i.e. more than one packet exchange in the area covered by a transmission), and it facilitates the integration of new physical layer capacity increasing technologies.
HAMILTONIAN PROPERTIES OF FAULTY RECURSIVE CIRCULANT GRAPHS
Authors: TSAI CHANG-HSIUNG , TAN JIMMY J. M. , CHUANG YEN-CHU , HSU LIH-HSING
Published: February 2003

We present some results concerning hamiltonian properties of recursive circulant graphs in the presence of faulty vertices and/or edges. The recursive circulant graph G(N, d) with d ≥ 2 has vertex set V(G) = {0, 1, …, N - 1} and the edge set E(G) = {(v, w)| ∃ i, 0 ≤ i ≤ ⌈ log d N⌉ - 1, such that v = w + di (mod N)}. When N = cdk where d ≥ 2 and 2 ≤ c ≤ d, G(cdk, d) is regular, node symmetric and can be recursively constructed. G(cdk, d) is a bipartite graph if and only if c is even and d is odd. Let F, the faulty set, be a subset of V(G(cdk, d)) ∪ E(G(cdk, d)). In this paper, we prove that G(cdk, d) - F remains hamiltonian if |F| ≤ deg (G(cdk, d)) - 2 and G(cdk, d) is not bipartite. Moreover, if |F| ≤ deg (G(cdk, d)) - 3 and G(cdk, d) is not a bipartite graph, we prove a more stronger result that for any two vertices u and v in V(G(cdk, d)) - F, there exists a hamiltonian path of G(cdk, d) - F joining u and v.
Higher-Order Statistics of Input Ensembles and the Response of Simple Model Neurons
Authors: Kuhn Alexandre , Aertsen Ad , Rotter Stefan
Published: February 2003

Pairwise correlations among spike trains recorded in vivo have been frequently reported. It has been argued that correlated activity could play an important role in the brain, because it efficiently modulates the response of a postsynaptic neuron. We show here that a neuron's output firing rate critically depends on the higher-order statistics of the input ensemble. We constructed two statistical models of populations of spiking neurons that fired with the same rates and had identical pairwise correlations, but differed with regard to the higher-order interactions within the population. The first ensemble was characterized by clusters of spikes synchronized over the whole population. In the second ensemble, the size of spike clusters was, on average, proportional to the pairwise correlation. For both input models, we assessed the role of the size of the population, the firing rate, and the pairwise correlation on the output rate of two simple model neurons: a continuous firing-rate model and a conductance-based leaky integrate-and-fire neuron. An approximation to the mean output rate of the firing-rate neuron could be derived analytically with the help of shot noise theory. Interestingly, the essential features of the mean response of the two neuron models were similar. For both neuron models, the three input parameters played radically different roles with respect to the postsynaptic firing rate, depending on the interaction structure of the input. For instance, in the case of an ensemble with small and distributed spike clusters, the output firing rate was efficiently controlled by the size of the input population. In addition to the interaction structure, the ratio of inhibition to excitation was found to strongly modulate the effect of correlation on the postsynaptic firing rate.