bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of the MtrC-MtrD-MtrE Efflux Pump Due to an
mtrR
Mutation Is Required for Chromosomally Mediated Penicillin Resistance in
Neisseria gonorrhoeae
Authors: Veal Wendy L. , Nicholas Robert A. , Shafer William M.
Published: September 2002

The importance of the
mtrCDE
-encoded efflux pump in conferring chromosomally mediated penicillin resistance on certain strains of
Neisseria gonorrhoeae
was determined by using genetic derivatives of penicillin-sensitive strain FA19 bearing defined mutations (
mtrR
,
penA
, and
penB
) donated by a clinical isolate (FA6140) expressing high-level resistance to penicillin and antimicrobial hydrophobic agents (HAs). When introduced into strain FA19 by transformation, a single base pair deletion in the
mtrR
promoter sequence from strain FA6140 was sufficient to provide high-level resistance to HAs (e.g., erythromycin and Triton X-100) but only a twofold increase in resistance to penicillin. When subsequent mutations in
penA
and
porIB
were introduced from strain FA6140 into strain WV30 (FA19
mtrR
) by transformation, resistance to penicillin increased incrementally up to a MIC of 1.0 μg/ml. Insertional inactivation of the gene (
mtrD
) encoding the membrane transporter component of the Mtr efflux pump in these transformant strains and in strain FA6140 decreased the MIC of penicillin by 16-fold. Genetic analyses revealed that
mtrR
mutations, such as the single base pair deletion in its promoter, are needed for phenotypic expression of penicillin and tetracycline resistance afforded by the
penB
mutation. As
penB
represents amino acid substitutions within the third loop of the outer membrane PorIB protein that modulate entry of penicillin and tetracycline, the results presented herein suggest that PorIB and the MtrC-MtrD-MtrE efflux pump act synergistically to confer resistance to these antibiotics.
Deficiency of aSinorhizobium meliloti bacAMutant in Alfalfa Symbiosis Correlates with Alteration of the Cell Envelope
Authors: Ferguson Gail P. , Roop R. Martin , Walker Graham C.
Published: September 2002

The BacA protein is essential for the long-term survival ofSinorhizobium melilotiandBrucella abortuswithin acidic compartments in plant and animal cells, respectively. Since both theS. melilotiandB. abortus bacAmutants have an increased resistance to bleomycin, it was hypothesized that BacA was a transporter of bleomycin and bleomycin-like compounds into the bacterial cell. However, our finding that theS. meliloti bacAmutant also has an increased sensitivity to detergents, a hydrophobic dye, ethanol, and acid pH supported a model in which BacA function affects the bacterial cell envelope. In addition, anS. meliloti lpsBmutant that is defective at a stage in infection of the host similar to that found for abacAmutant is also sensitive to the same agents, and the carbohydrate content of its lipopolysaccharide (LPS) is altered. However, analysis of crude preparations of thebacAmutant LPS suggested that, unlike that for LpsB, BacA function did not affect the carbohydrate composition of the LPS. Rather, we found that at least one function of BacA is to affect the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the α-proteobacteria, includingB. abortus.
Divergent Structure and Regulatory Mechanism of Proline Catabolic Systems: Characterization of the
putAP
Proline Catabolic Operon of
Pseudomonas aeruginosa
PAO1 and Its Regulation by PruR, an AraC/XylS Family Protein
Authors: Nakada Yuji , Nishijyo Takayuki , Itoh Yoshifumi
Published: September 2002

Pseudomonas aeruginosa
PAO1 utilizes proline as the sole source of carbon and nitrogen via a bifunctional enzyme (the
putA
gene product) that has both proline dehydrogenase (EC 1.5.99.8) and pyrroline 5-carboxylate dehydrogenase (EC 1.5.1.12) activities. We characterized the
pruR-putAP
loci encoding the proline catabolic system of this strain. In contrast to the
putA
and
putP
(encoding proline permease) genes of other gram- negative bacteria, which are located at divergent or separate loci, Northern blotting demonstrated that the two genes form an operon in strain PAO1. While the phylogenetic lineage of the PutP protein of strain PAO1 was related to that of the origin (80% identity to the
P. putida
counterpart), PutA of PAO1 (PutA
PAO
) was rather distantly related (47% identity) to the
P. putida
counterpart. Moreover, unlike the PutA proteins of
P. putida
and enteric bacteria, PutA
PAO
appeared to lack a regulatory function. Upstream of the
putAP
operon, the divergent PA0781 gene specified a hypothetical outer membrane protein with a molecular weight of 74,202. This gene appeared to be dispensable for proline utilization as indicated by the normal growth of a knockout mutant of PA0781 on medium containing proline. The
pruR
(proline utilization regulator) gene immediately upstream of PA0781 encoded a transcriptional activator of the AraC/XylS protein family and mediated the proline-responsive expression of
putAP.
Primer extension studies identified a PruR-dependent promoter responsive to proline in the 5′-flanking region of
putA.
Thus, the proline utilization system of
P. aeruginosa
differs from that of
P. putida
with respect to
putA
structure, the organization of the
putAP
genes, and the regulatory mechanism of
putA
expression.
Adaptive, or Stationary-Phase, Mutagenesis, a Component of Bacterial Differentiation in
Bacillus subtilis
Authors: Sung Huang-Mo , Yasbin Ronald E.
Published: September 2002

Adaptive (stationary-phase) mutagenesis occurs in the gram-positive bacterium
Bacillus subtilis
. Furthermore, taking advantage of
B. subtilis
as a paradigm for the study of prokaryotic differentiation and development, we have shown that this type of mutagenesis is subject to regulation involving at least two of the genes that are involved in the regulation of post-exponential phase prokaryotic differentiation, i.e.,
comA
and
comK
. On the other hand, a functional RecA protein was not required for this type of mutagenesis. The results seem to suggest that a small subpopulation(s) of the culture is involved in adaptive mutagenesis and that this subpopulation(s) is hypermutable. The existence of such a hypermutable subpopulation(s) raises important considerations with respect to evolution, the development of specific mutations, the nature of bacterial populations, and the level of communication among bacteria in an ecological niche.
A CheW Homologue Is Required for
Myxococcus xanthus
Fruiting Body Development, Social Gliding Motility, and Fibril Biogenesis
Authors: Bellenger Kristen , Ma Xiaoyuan , Shi Wenyuan , Yang Zhaomin
Published: September 2002

In bacteria with multiple sets of chemotaxis genes, the deletion of homologous genes or even different genes in the same operon can result in disparate phenotypes.
Myxococcus xanthus
is a bacterium with multiple sets of chemotaxis genes and/or homologues. It was shown previously that
difA
and
difE
, encoding homologues of the methyl-accepting chemoreceptor protein (MCP) and the CheA kinase, respectively, are required for
M. xanthus
social gliding (S) motility and development. Both
difA
and
difE
mutants were also defective in the biogenesis of the cell surface appendages known as extracellular matrix fibrils. In this study, we investigated the roles of the CheW homologue encoded by
difC
, a gene at the same locus as
difA
and
difE
. We showed that
difC
mutations resulted in defects in
M. xanthus
developmental aggregation, sporulation, and S motility. We demonstrated that
difC
is indispensable for wild-type cellular cohesion and fibril biogenesis but not for pilus production. We further illustrated the ectopic complementation of a
difC
in-frame deletion by a wild-type
difC
. The identical phenotypes of
difA
,
difC
, and
difE
mutants are consistent and supportive of the hypothesis that the Dif chemotaxis homologues constitute a chemotaxis-like signal transduction pathway that regulates
M. xanthus
fibril biogenesis and S motility.
A Novel Class of Heat and Secretion Stress-Responsive Genes Is Controlled by the Autoregulated CssRS Two-Component System ofBacillus subtilis
Authors: Darmon Elise , Noone David , Masson Anne , Bron Sierd , Kuipers Oscar P. , Devine Kevin M. , Dijl Jan Maarten van
Published: September 2002

Bacteria need dedicated systems that allow appropriate adaptation to the perpetual changes in their environments. InBacillus subtilis, two HtrA-like proteases, HtrA and HtrB, play critical roles in the cellular response to secretion and heat stresses. Transcription of these genes is induced by the high-level production of a secreted protein or by a temperature upshift. The CssR-CssS two-component regulatory system plays an essential role in this transcriptional activation. Transcription of thecssRSoperon is autoregulated and can be induced by secretion stress, by the absence of either HtrA or HtrB, and by heat stress in a HtrA null mutant strain. Two start sites are used forcssRStranscription, only one of which is responsive to heat and secretion stress. The divergently transcribedhtrBandcssRSgenes share a regulatory region through which their secretion and heat stress-induced expression is linked. This study shows that CssRS-regulated genes represent a novel class of heat-inducible genes, which is referred to as class V and currently includes two genes:htrAandhtrB.
Expression of the
Azotobacter vinelandii
Poly-β-Hydroxybutyrate Biosynthetic
phbBAC
Operon Is Driven by Two Overlapping Promoters and Is Dependent on the Transcriptional Activator PhbR
Authors: Peralta-Gil Martín , Segura Daniel , Guzmán Josefina , Servín-González Luis , Espín Guadalupe
Published: September 2002

The
Azotobacter vinelandii phbBAC
genes encode the enzymes for poly-β-hydroxybutyrate (PHB) synthesis. The
phbR
gene, which is located upstream of and in the opposite direction of
phbBAC
, encodes PhbR, a transcriptional activator which is a member of the AraC family of activators. Here we report that a mutation in
phbR
reduced PHB accumulation and transcription of a
phbB
-
lacZ
fusion. We also report that
phbB
is transcribed from two overlapping promoters, p
B
1 and p
B
2. The region corresponding to the −35 region of p
B
1 overlaps the p
B
2 −10 region. In the
phbR
mutant, expression of
phbB
from the p
B
1 promoter is significantly reduced, whereas expression from the p
B
2 promoter is slightly increased. Two
phbR
promoters, p
R
1 and p
R
2, were also identified. Transcription from p
R
2 was shown to be dependent on σ
S
. Six conserved 18-bp sites, designated R1 to R6, are present within the
phbR-phbB
intergenic region and are proposed to be putative binding targets for PhbR. R1 overlaps the −35 region of the p
B
1 promoter. A model for the regulation of
phbB
transcription by PhbR is proposed.
Biofilm Formation and Acyl Homoserine Lactone Production in the
Burkholderia cepacia
Complex
Authors: Conway Barbara-Ann D. , Venu Vicnays , Speert David P.
Published: September 2002

Acyl homoserine lactone (acyl-HSL)-mediated gene regulation has been shown to influence biofilm formation in one
Burkholderia cepacia
cystic fibrosis isolate, but it is not known whether this relationship is a consistent feature of the several genomic species that make up the
B. cepacia
complex (BCC). We screened strains belonging to genomovars I to V of the BCC for biofilm formation on an abiotic surface and for acyl-HSL synthesis. We determined that organisms from each of these genomovars were capable of biofilm formation. Similarly, acyl-HSL was synthesized by organisms from each of genomovars I to V, with most isolates producing octanoyl-HSL in greatest abundance. When biofilms were grown in Luria broth, acyl-HSL synthesis and biofilm formation appeared to be associated, but these phenotypes were independent when the biofilms were grown in basal salts containing citrate. Genomovar V strains synthesized the greatest quantities of acyl-HSL, and genomovar II and III-A strains elaborated the most abundant biofilms. Quorum sensing may play a role in BCC pathogenesis, but it may not regulate biofilm formation under all growth conditions.
Characterization of theSinorhizobium meliloti sinR/sinILocus and the Production of NovelN-Acyl Homoserine Lactones
Authors: Marketon Melanie M. , Gronquist Matthew R. , Eberhard Anatol , González Juan E.
Published: September 2002

Sinorhizobium melilotiis a soil bacterium which can establish a nitrogen-fixing symbiosis with the legumeMedicago sativa. Recent work has identified a pair of genes,sinRandsinI, which represent a potential quorum-sensing system and are responsible for the production ofN-acyl homoserine lactones (AHLs) in twoS. melilotistrains, Rm1021 and Rm41. In this work, we characterize thesinRIlocus and show that these genes are responsible for the synthesis of several long-chain AHLs ranging from 12 to 18 carbons in length. Four of these, 3-oxotetradecanoyl HL, 3-oxohexadecenoyl HL, hexadecenoyl HL, and octadecanoyl HL, have novel structures. This is the first report of AHLs having acyl chains longer than 14 carbons. We show that a disruption insinIeliminates these AHLs and that asinRdisruption results in only basal levels of the AHLs. Moreover, the samesinIandsinRmutations also lead to a decrease in the number of pink nodules during nodulation assays, as well as a slight delay in the appearance of pink nodules, indicating a role for quorum sensing in symbiosis. We also show thatsinIandsinRmutants are still capable of producing several short-chain AHLs, one of which was identified as octanoyl HL. We believe that these short-chain AHLs are evidence of a second quorum-sensing system in Rm1021, which we refer to here as themelsystem, for “S. meliloti.”
YfcX Enables Medium-Chain-Length Poly(3-Hydroxyalkanoate) Formation from Fatty Acids in Recombinant
Escherichia coli fadB
Strains
Authors: Snell Kristi D. , Feng Feng , Zhong Luhua , Martin David , Madison Lara L.
Published: September 2002

Expression of
Escherichia coli
open reading frame
yfcX
is shown to be required for medium-chain-length polyhydroxyalkanoate (PHA
MCL
) formation from fatty acids in an
E. coli fadB
mutant. The open reading frame encodes a protein, YfcX, with significant similarity to the large subunit of multifunctional β-oxidation enzymes.
E. coli fadB
strains modified to contain an inactivated copy of
yfcX
and to express a medium-chain-length synthase are unable to form PHA
MCL
s when grown in the presence of fatty acids. Plasmid-based expression of
yfcX
in the FadB
−
YfcX
−
PhaC
+
strain restores polymer formation. YfcX is shown to be a multifunctional enzyme that minimally encodes hydratase and dehydrogenase activities. The gene encoding YfcX is located downstream from
yfcY
, a gene encoding thiolase activity. Results of insertional inactivation studies and enzyme activity analyses suggest a role for
yfcX
in PHA monomer unit formation in recombinant
E. coli fadB
mutant strains. Further studies are required to determine the natural role of YfcX in the metabolism of
E. coli
.
Genes Encoding Specific Nickel Transport Systems Flank the Chromosomal Urease Locus of Pathogenic Yersiniae
Authors: Sebbane Florent , Mandrand-Berthelot Marie-Andrée , Simonet Michel
Published: September 2002

The transition metal nickel is an essential cofactor for a number of bacterial enzymes, one of which is urease. Prior to its incorporation into metalloenzyme active sites, nickel must be imported into the cell. Here, we report identification of two loci corresponding to nickel-specific transport systems in the gram-negative, ureolytic bacterium
Yersinia pseudotuberculosis
. The loci are located on each side of the chromosomal urease gene cluster
ureABCEFGD
and have the same orientation as the latter. The
yntABCDE
locus upstream of the
ure
genes encodes five predicted products with sequence homology to ATP-binding cassette nickel permeases present in several gram-negative bacteria. The
ureH
gene, located downstream of
ure
, encodes a single-component carrier which displays homology to polypeptides of the nickel-cobalt transporter family. Transporters with homology to these two classes are also present (again in proximity to the urease locus) in the other two pathogenic yersiniae,
Y. pestis
and
Y. enterocolitica
. An
Escherichia coli nikA
insertion mutant recovered nickel uptake ability following heterologous complementation with either the
ynt
or the
ureH
plasmid-borne gene of
Y. pseudotuberculosis
, demonstrating that each carrier is necessary and sufficient for nickel transport. Deletion of
ynt
in
Y. pseudotuberculosis
almost completely abolished bacterial urease activity, whereas deletion of
ureH
had no effect. Nevertheless, rates of nickel transport were significantly altered in both
ynt
and
ureH
mutants. Furthermore, the
ynt ureH
double mutant was totally devoid of nickel uptake ability, thus indicating that Ynt and UreH constitute the only routes for nickel entry. Both Ynt and UreH show selectivity for Ni
2+
ions. This is the first reported identification of genes coding for both kinds of nickel-specific permeases situated adjacent to the urease gene cluster in the genome of a microorganism.
Differential Expression of Two Catechol 1,2-Dioxygenases in
Burkholderia
sp. Strain TH2
Authors: Suzuki Katsuhisa , Ichimura Atsushi , Ogawa Naoto , Hasebe Akira , Miyashita Kiyotaka
Published: September 2002

Burkholderia
sp. strain TH2, a 2-chlorobenzoate (2CB)-degrading bacterium, metabolizes benzoate (BA) and 2CB via catechol. Two different gene clusters for the catechol
ortho
-cleavage pathway (
cat1
and
cat2
) were cloned from TH2 and analyzed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis showed that while both catechol dioxygenases (CatA1 and CatA2) were produced in BA-grown cells, CatA1 was undetectable when strain TH2 was grown on 2CB or
cis
,
cis
-muconate (CCM), an intermediate of catechol degradation. However, production of CatA1 during growth on 2CB or CCM was observed when
cat
2 genes were disrupted. The difference in the production of CatA1 and CatA2 was apparently due to a difference in inducer recognition by the regulators of the gene clusters. The inducer of CatA1 was found to be BA, not 2CB, by using a 2-halobenzoate dioxygenase gene (
cbd
) disruptant, which is incapable of transforming (chloro)benzoate. It was also found that CCM or its metabolite acts as an inducer for CatA2. When
cat2
genes were disrupted, the growth rate in 2CB culture was reduced while that in BA culture was not. These results suggest that although
cat2
genes are not indispensable for growth of TH2 on 2CB, they are advantageous.
Construction and Characterization of Transposon Insertion Mutations inCorynebacterium diphtheriaeThat Affect Expression of the Diphtheria Toxin Repressor (DtxR)
Authors: Oram Diana Marra , Avdalovic Ana , Holmes Randall K.
Published: September 2002

Transcription of the bacteriophage-borne diphtheria toxin genetoxis negatively regulated, in response to intracellular Fe2+concentration, by the chromosomally encoded diphtheria toxin repressor (DtxR). Due to a scarcity of tools, genetic analysis ofCorynebacterium diphtheriaehas primarily relied on analysis of chemically induced and spontaneously occurring mutants and on the results of experiments withC. diphtheriaegenes cloned inEscherichia colior analyzed in vitro. We modified a Tn5-based mutagenesis technique for use withC. diphtheriae, and we used it to construct the first transposon insertion libraries in the chromosome of this gram-positive pathogen. We isolated two insertions that affected expression of DtxR, one 121 bp upstream ofdtxRand the other within an essential region of thedtxRcoding sequence, indicating for the first time thatdtxRis a dispensable gene inC. diphtheriae. Both mutant strains secrete diphtheria toxin when grown in medium containing sufficient iron to repress secretion of diphtheria toxin by wild-typeC. diphtheriae. The upstream insertion mutant still produces DtxR in decreased amounts and regulates siderophore secretion in response to iron in a manner similar to its wild-type parent. The mutant containing the transposon insertion withindtxRdoes not produce DtxR and overproduces siderophore in the presence of iron. Differences in the ability of the two mutant strains to survive oxidative stress also indicated that the upstream insertion retained slight DtxR activity, whereas the insertion withindtxRabolished DtxR activity. This is the first evidence that DtxR plays a role in protecting the cell from oxidative stress.
Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures
Authors: Ma Jiong , Campbell Allan , Karlin Samuel
Published: September 2002

This work assesses relationships for 30 complete prokaryotic genomes between the presence of the Shine-Dalgarno (SD) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. A significant positive correlation of the presence of an SD sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong SD sequence than average genes. Genes with AUG start codons are more likely than genes with other start codons, GUG or UUG, to possess an SD sequence. Genes in close proximity to upstream genes on the same coding strand in most genomes are significantly higher in SD presence. In light of these results, we discuss the role of the SD sequence in translation initiation and its relationship with predicted gene expression levels and with operon structure in both bacterial and archaeal genomes.
The
Streptomyces
Genome Contains Multiple Pseudo-
attB
Sites for the φC31-Encoded Site-Specific Recombination System
Authors: Combes Patricia , Till Rob , Bee Sally , Smith Margaret C. M.
Published: September 2002

The integrase from the
Streptomyces
phage φC31 is a member of the serine recombinase family of site-specific recombinases and is fundamentally different from that of λ or its relatives. Moreover, φC31
int
/
attP
is used widely as an essential component of integration vectors (such as pSET152) employed in the genetic analysis of
Streptomyces
species. φC31 or integrating plasmids containing
int
/
attP
have been shown previously to integrate at a locus,
attB
, in the chromosome. The DNA sequences of the
attB
sites of various
Streptomyces
species revealed nonconserved positions. In particular, the crossover site was narrowed to the sequence 5′TT present in both
attP
and
attB
. Strains of
Streptomyces coelicolor
and
S. lividans
were constructed with a deletion of the
attB
site (Δ
attB
), and pSET152 was introduced into these strains by conjugation. Thus, secondary or pseudo-
attB
sites were identified by Southern blotting and after rescue of plasmids containing DNA flanking the insertion sites from the chromosome. The sequences of the integration sites had similarity to those of
attB
. Analysis of the insertions of pSET152 into both

attB
+

and Δ
attB
strains indicated that this plasmid can integrate at several loci via independent recombination events within a transconjugant.
Molecular Characterization of DSR-E, an α-1,2 Linkage-Synthesizing Dextransucrase with Two Catalytic Domains
Authors: Bozonnet Sophie , Dols-Laffargue Marguerite , Fabre Emeline , Pizzut Sandra , Remaud-Simeon Magali , Monsan Pierre , Willemot René-Marc
Published: September 2002

A novelLeuconostoc mesenteroidesNRRL B-1299 dextransucrase gene,dsrE, was isolated, sequenced, and cloned inEscherichia coli, and the recombinant enzyme was shown to be an original glucansucrase which catalyses the synthesis of α-1,6 and α-1,2 linkages. The nucleotide sequence of thedsrEgene consists of an open reading frame of 8,508 bp coding for a 2,835-amino-acid protein with a molecular mass of 313,267 Da. This is twice the average mass of the glucosyltransferases (GTFs) known so far, which is consistent with the presence of an additional catalytic domain located at the carboxy terminus of the protein and of a central glucan-binding domain, which is also significantly longer than in other glucansucrases. From sequence comparison with family 70 and α-amylase enzymes, crucial amino acids involved in the catalytic mechanism were identified, and several original sequences located at some highly conserved regions in GTFs were observed in the second catalytic domain.
Escherichia coli
DegP Protease Cleaves between Paired Hydrophobic Residues in a Natural Substrate: the PapA Pilin
Authors: Jones C. Hal , Dexter Paul , Evans Amy K. , Liu Christopher , Hultgren Scott J. , Hruby Dennis E.
Published: September 2002

The DegP protein, a multifunctional chaperone and protease, is essential for clearance of denatured or aggregated proteins from the inner-membrane and periplasmic space in
Escherichia coli.
To date, four natural targets for DegP have been described: colicin A lysis protein, pilin subunits and MalS from
E. coli
, and high-molecular-weight adherence proteins from
Haemophilus influenzae.
In vitro, DegP has shown weak protease activity with casein and several other nonnative substrates. We report here the identification of the major pilin subunit of the Pap pilus, PapA, as a natural DegP substrate and demonstrate binding and proteolysis of this substrate in vitro. Using overlapping peptide arrays, we identified three regions in PapA that are preferentially cleaved by DegP. A 7-mer peptide was found to be a suitable substrate for cleavage by DegP in vitro. In vitro proteolysis of model peptide substrates revealed that cleavage is dependent upon the presence of paired hydrophobic amino acids; moreover, cleavage was found to occur between the hydrophobic residues. Finally, we demonstrate that the conserved carboxyl-terminal sequence in pilin subunits, although not a cleavage substrate for DegP, activates the protease and we propose that the activating peptide is recognized by DegP's PDZ domains.
Pseudoknot-Dependent Translational Coupling inrepBAGenes of the IncB Plasmid pMU720 Involves Reinitiation
Authors: Praszkier J. , Pittard A. J.
Published: September 2002

Replication of the IncB miniplasmid pMU720 requires synthesis of the replication initiator protein, RepA, whose translation is coupled to that of a leader peptide, RepB. The unusual feature of this system is that translational coupling inrepBAhas to be activated by the formation of a pseudoknot immediately upstream of therepAShine-Dalgarno sequence. A small antisense RNA, RNAI, controls replication of pMU720 by interacting withrepBAmRNA to inhibit expression ofrepAboth directly, by preventing formation of the pseudoknot, and indirectly, by inhibiting translation ofrepB. The mechanism of translational coupling inrepBAwas investigated using the specialized ribosome system, which directs a subpopulation of ribosomes that carry an altered anti-Shine-Dalgarno sequence to translate mRNA molecules whose Shine-Dalgarno sequences have been altered to be complementary to the mutant anti-Shine-Dalgarno sequence. Our data indicate that translation ofrepAinvolves reinitiation by the ribosome that has terminated translation ofrepB. The role of the pseudoknot in this process and its effect on the control of copy number in pMU720 are discussed.
The Positive Regulator, TraJ, of the
Escherichia coli
F Plasmid Is Unstable in a
cpxA
* Background
Authors: Gubbins Michael J. , Lau Isabella , Will William R. , Manchak Janet M. , Raivio Tracy L. , Frost Laura S.
Published: September 2002

The Cpx (conjugative plasmid expression) stress response of
Escherichia coli
is induced in response to extracytoplasmic signals generated in the cell envelope, such as misfolded proteins in the periplasm. Detection of stress is mediated by the membrane-bound histidine kinase, CpxA. Signaling of the response regulator CpxR by activated CpxA results in the expression of several factors required for responding to cell envelope stress. CpxA was originally thought to be required for the expression of the positive regulator of the F plasmid transfer (
tra
) operon, TraJ. It was later determined that constitutive gain-of-function mutations in
cpxA
led to activation of the Cpx envelope stress response and decreased TraJ expression. In order to determine the nature of the downregulation of TraJ, the level of expression of TraJ, TraM, and TraY, the F-encoded regulatory proteins of the F
tra
region, was determined both in a
cpxA
* background and in a wild-type background in which the Cpx stress response was induced by overexpression of the outer membrane lipoprotein, NlpE. Our results suggest that TraJ downregulation is controlled by a posttranscriptional mechanism that operates in the cytoplasm in response to upregulation of the Cpx stress response by both the
cpxA
* gain-of-function mutation and the overexpression of NlpE.
Conserved Response Regulator CtrA and IHF Binding Sites in the α-Proteobacteria
Caulobacter crescentus
and
Rickettsia prowazekii
Chromosomal Replication Origins
Authors: Brassinga Ann Karen C. , Siam Rania , McSween William , Winkler Herbert , Wood David , Marczynski Gregory T.
Published: September 2002

CzcR is the
Rickettsia prowazekii
homolog of the
Caulobacter crescentus
global response regulator CtrA. CzcR expression partially compensates for developmental defects in
ctrA
mutant
C. crescentus
cells, and CzcR binds to all five CtrA binding sites in the
C. crescentus
replication origin. Conversely, CtrA binds to five similar sites in the putative
R. prowazekii
replication origin (
oriRp
). Also,
Escherichia coli
IHF protein binds over a central CtrA binding site in
oriRp
. Therefore, CtrA and IHF regulatory proteins have similar binding patterns in both replication origins, and we propose that CzcR is a global cell cycle regulator in
R. prowazekii
.
Analysis of the Conjugal Transfer System of the Pheromone- Independent Highly Transferable Enterococcus Plasmid pMG1: Identification of a
tra
Gene (
traA
) Up-Regulated during Conjugation
Authors: Tanimoto Koichi , Ike Yasuyoshi
Published: September 2002

pMG1 (65.1 kbp) is a pheromone-independent
Enterococcus faecium
conjugative plasmid conferring gentamicin resistance. pMG1 is able to transfer to enterococci at a high frequency in broth mating experiments, and it does not respond to the sex pheromones which are involved in the high-frequency transfer system of some conjugative plasmids in
Enterococcus faecalis
. To analyze regulation of
tra
gene expression in pMG1, transcripts of pMG1 were examined during conjugation. RNA samples were prepared from mating mixtures 20, 40, 80, and 160 min after initiation of mating and were subsequently analyzed by Northern hybridization by using a variety of pMG1 DNA fragments as probes. One transcript of gene 71ORF2 increased to the maximal level 20 min after the start of mating. The level of this transcript decreased after 40 min of mating to the same level as the level in the control donor culture. The increase was not observed in cultures of the donor cells or recipient cells. These findings suggested that the increase was a conjugation-specific event. The 71ORF2 gene of pMG1 was disrupted by using the suicide vector pMG226 carrying an erythromycin resistance gene that is expressed in enterococci. The transfer frequencies of mutant plasmid pMG229, which had a disrupted 71ORF2 gene in pMG1, and the parent plasmid pMG1 were 1.6 × 10
−7
and 1.1 × 10
−3
per donor cell, respectively, in broth mating experiments, and the transfer frequencies of pMG229 and pMG1 were 2.7 × 10
−3
and 8.5 × 10
−2
per donor cell, respectively, in filter mating experiments. This indicated that the transfer frequency of plasmid pMG229 was reduced during broth mating and was not altered during filter mating. 71ORF2, which is designated
traA
, is a gene involved in the
tra
gene system for conjugation, and the product of this gene is associated with the formation or stabilization of mating aggregates during broth mating.
Evidence for Conformational Protection of Nitrogenase against Oxygen in
Gluconacetobacter diazotrophicus
by a Putative FeSII Protein
Authors: Ureta Alejandro , Nordlund Stefan
Published: September 2002

The mechanisms protecting nitrogenase in
Gluconacetobacter diazotrophicus
from damage by oxygen were studied. Evidence is provided suggesting that in
G. diazotrophicus
these mechanisms include respiratory protection as well as conformational protection in which a putative FeSII Shethna protein is involved.
Novel Locus Required for Expression of High-Level Macrolide-Lincosamide-Streptogramin B Resistance in
Staphylococcus aureus
Authors: Martin P. K. , Bao Y. , Boyer E. , Winterberg K. M. , McDowell L. , Schmid M. B. , Buysse J. M.
Published: September 2002

The
yycF1
(Ts) mutation in
Staphylococcus aureus
conferred hypersensitivity to macrolide-lincosamide-streptogramin B (MLS
B
) antibiotics on strains either containing or lacking
ermB
. The overexpression of the
S. aureus
Ssa protein restored the
yycF1
mutant to wild-type levels of susceptibility. Inactivation of
ssa
in an unmutagenized strain dramatically reduced
ermB
-based resistance. Conditional loss of function or expression of
ssa
in the
yycF1
mutant is proposed to result in the observed hypersensitivity to MLS
B
antibiotics.
Secretion of α-Amylase from
Pseudoalteromonas haloplanktis
TAB23: Two Different Pathways in Different Hosts
Authors: Tutino Maria Luisa , Parrilli Ermenegilda , Giaquinto Laura , Duilio Angela , Sannia Giovanni , Feller Georges , Marino Gennaro
Published: September 2002

Secretion of cold-adapted α-amylase from
Pseudoalteromonas haloplanktis
TAB23 was studied in three Antarctic bacteria. We demonstrated that the enzyme is specifically secreted in the psychrophilic hosts even in the absence of a protein domain that has been previously reported to be necessary for α-amylase secretion in
Escherichia coli
. The occurrence of two different secretion pathways in different hosts is proposed.
CONSTRUCTING A QUERY-ABLE RADIAL BASIS FUNCTION ARTIFICIAL NEURAL NETWORK
Authors: AUGUSTEIJN MARIJKE F. , SHAW KELLY A.
Published: September 2002

Artificial neural networks will be more widely accepted as standard engineering tools if their reasoning process can be made less opaque. This paper describes NetQuery, an explanation mechanism that extracts meaningful explanations from trained Radial Basis Function (RBF) networks. RBF networks are well suited for explanation generation because they contain a set of locally tuned units. Standard RBF networks are modified to identify dependencies between the inputs, to be sparsely connected, and to have an easily interpretable output layer. Given these modifications, the network architecture can be used to extract "Why?" and "Why not?" explanations from the network in terms of excitatory and inhibitory in-puts and their linear relationships, greatly simplified by a run-time pruning algorithm. These query results are validated by creating an expert system based on the explanations. NetQuery is also able to inform a user about a possible change in category for a given pattern by responding to a "How can I…?" query. This kind of query is extremely useful when analyzing the quality of a pattern set.
IMPROVED BACKPROPAGATION LEARNING IN NEURAL NETWORKS WITH WINDOWED MOMENTUM
Authors: ISTOOK ERNEST , MARTINEZ TONY
Published: September 2002

Backpropagation, which is frequently used in Neural Network training, often takes a great deal of time to converge on an acceptable solution. Momentum is a standard technique that is used to speed up convergence and maintain generalization performance. In this paper we present the Windowed Momentum algorithm, which increases speedup over Standard Momentum. Windowed Momentum is designed to use a fixed width history of recent weight updates for each connection in a neural network. By using this additional information, Windowed Momentum gives significant speedup over a set of applications with same or improved accuracy. Windowed Momentum achieved an average speedup of 32% in convergence time on 15 data sets, including a large OCR data set with over 500,000 samples. In addition to this speedup, we present the consequences of sample presentation order. We show that Windowed Momentum is able to overcome these effects that can occur with poor presentation order and still maintain its speedup advantages.
EXTRACTING THE PRINCIPAL BEHAVIOR OF A PROBABILISTIC SUPERVISOR THROUGH NEURAL NETWORKS ENSEMBLE
Authors: HARTONO PITOYO , HASHIMOTO SHUJI
Published: September 2002

In this paper, we propose a model of a neural network ensemble that can be trained with a supervisor having two kinds of input-output functions where the occurrence probability of each function is not even. This condition can be likened to a learning condition, in which the learning data are hampered by noise. In this case, the neural network has the impression that the learning supervisor (object) has a probabilistic behavior in which the supervisor generates correct learning data most of the time but occasionally generates erroneous ones. The objective is to train the neural network to approximate the greatest distributed input-output relation, which can be considered to be the principal nature of the supervisor, so that we can obtain a neural network that is able, to some extent, to suppress the ill effect of erroneous data encountered during the learning process.
A DISCRETE FULLY RECURRENT NETWORK OF MAX PRODUCT UNITS FOR ASSOCIATIVE MEMORY AND CLASSIFICATION
Authors: BROUWER ROELOF K.
Published: September 2002

This paper defines the truncated normalized max product operation for the transformation ofstates of a network and provides a method for solving a set of equations based on this operation. The operation serves as the transformation for the set of fully connected units in a recurrent network that otherwise might consist of linear threshold units. Component values of the state vector and ouputs of the units take on the values in the set {0, 0.1, …, 0.9, 1}. The result is a much larger state space given a particular number of units and size of connection matrix than for a network based on threshold units. Since the operation defined here can form the basis of transformations in a recurrent network with a finite number of states, fixed points or cycles are possible and the network based on this operation for transformations can be used as an associative memory or pattern classifier with fixed points taking on the role of prototypes. Discrete fully recurrent networks have proven themselves to be very useful as associative memories and as classifiers. However they are often based on units that have binary states. The effect of this is that the data to be processed consisting of vectors in ℜnhave to be converted to vectors in {0, 1}mwith m much larger than n since binary encoding based on positional notation is not feasible. This implies a large increase in the number of components. The effect can be lessened by allowing more states for each unit in our network. The network proposed demonstrates those properties that are desirable in an associative memory very well as the simulations show.
UNSUPERVISED NEURAL LEARNING ON LIE GROUP
Authors: FIORI SIMONE
Published: September 2002

The present paper aims at introducing the concepts and mathematical details of unsupervised neural learning with orthonormality constrains. The neural structures considered are single non-linear layers and the learnable parameters are organized in matrices, as usual, which gives the parameters spaces the geometrical structure of the Euclidean manifold. The constraint of orthonormality for the connection-matrices further restricts the parameters spaces to differential manifolds such as the orthogonal group, the compact Stiefel manifold and its extensions. For these reasons, the instruments for characterizing and studying the behavior of learning equations for these particular networks are provided by the differential geometry of Lie groups. In particular, two sub-classes of the general Lie-group learning theories are studied in detail, dealing with first-order (gradient-based) and second-order (non-gradient-based) learning. Although the considered class of learning theories is very general, in the present paper special attention is paid to unsupervised learning paradigms.
STABILITY ANALYSIS OF HIGHER-ORDER NEURAL NETWORKS FOR COMBINATORIAL OPTIMIZATION
Authors: COOPER BRENTON
Published: September 2002

Recurrent neural networks with higher order connections, from here on referred to as higher-order neural networks (HONNs), may be used for the solution of combinatorial optimization problems. In Ref. 5 a mapping of the traveling salesman problem (TSP) onto a HONN of arbitrary order was developed, thereby creating a family of related networks that can be used to solve the TSP. In this paper, we explore the trade-off between network complexity and quality of solution that is made available by the HONN mapping of the TSP. The trade-off is investigated by undertaking an analysis of the stability of valid solutions to the TSP in a HONN of arbitrary order. The techniques used to perform the stability analysis are not new, but have been widely used elsewhere in the literature.15–17The original contribution in this paper is the application of these techniques to a HONN of arbitrary order used to solve the TSP. The results of the stability analysis show that the quality of solution is improved by increasing the network complexity, as measured by the order of the network. Furthermore, it is shown that the Hopfield network, as the simplest network in the family of higher-order networks, is expected to produce the poorest quality of solution.
NEURAL NETWORK BASED TEMPORAL VIDEO SEGMENTATION
Authors: CAO X. , SUGANTHAN P. N.
Published: September 2002

The organization of video information in video databases requires automatic temporal segmentation with minimal user interaction. As neural networks are capable of learning the characteristics of various video segments and clustering them accordingly, in this paper, a neural network based technique is developed to segment the video sequence into shots automatically and with a minimum number of user-defined parameters. We propose to employ growing neural gas (GNG) networks and integrate multiple frame difference features to efficiently detect shot boundaries in the video. Experimental results are presented to illustrate the good performance of the proposed scheme on real video sequences.
A NEURAL NETWORK APPROACH TO APPROXIMATING MAP IN BELIEF NETWORKS
Authors: PENG YUN , JIN MIAO
Published: September 2002

Bayesian belief networks (BBN) are a widely studied graphical model for representing uncertainty and probabilistic interdependence among variables. One of the factors that restricts the model's wide acceptance in practical applications is that the general inference with BBN is NP-hard. This is also true for the maximum a posteriori probability (MAP) problem, which is to find the most probable joint value assignment to all uninstantiated variables, given instantiation of some variables in a BBN . To circumvent the difficulty caused by MAP's computational complexity, we suggest in this paper a neural network approximation approach. With this approach, a BBN is treated as a neural network without any change or transformation of the network structure, and the node activation functions are derived based on an energy function defined over a given BBN. Three methods are developed. They are the hill-climbing style discrete method, the simulated annealing method, and the continuous method based on the mean field theory. All three methods are for BBN of general structures, with the restriction that nodes of BBN are binary variables. In addition, rules for applying these methods to noisy-or networks are also developed, which may lead to more efficient computation in some cases. These methods' convergence is analyzed, and their validity tested through a series of computer experiments with two BBN of moderate size and complexity. Although additional theoretical and empirical work is needed, the analysis and experiments suggest that this approach may lead to effective and accurate approximation for MAP problems.
RELATING PRIMING AND REPETITION SUPPRESSION
Authors: LÖRINCZ A. , SZIRTES G. , TAKÁCS B. , BIEDERMAN I. , VOGELS R.
Published: September 2002

We present a prototype of a recently proposed two stage model of the entorhinal–hippocampal loop. Our aim is to form a general computational model of the sensory neocortex. The model — grounded on pure information theoretic principles — accounts for the most characteristic features of long-term memory (LTM), performs bottom-up novelty detection, and supports noise filtering. Noise filtering can also serve to correct the temporal ordering of information processing. Surprisingly, as we examine the temporal characteristics of the model, the emergent dynamics can be interpreted as perceptual priming, a fundamental type of implicit memory. In the model's framework, computational results support the hypothesis of a strong correlation between perceptual priming and repetition suppression and this correlation is a direct consequence of the temporal ordering in forming the LTM. We also argue that our prototype offers a relatively simple and coherent explanation of priming and its relation to a general model of information processing by the brain.
TRAINING SIMULTANEOUS RECURRENT NEURAL NETWORK WITH RESILIENT PROPAGATION FOR STATIC OPTIMIZATION
Authors: SERPEN GURSEL , CORRA JOEL
Published: September 2002

This paper proposes a non-recurrent training algorithm, resilient propagation, for the Simultaneous Recurrent Neural network operating in relaxation-mode for computing high quality solutions of static optimization problems. Implementation details related to adaptation of the recurrent neural network weights through the non-recurrent training algorithm, resilient backpropagation, are formulated throughan algebraic approach. Performance of the proposed neuro-optimizer on a well-known static combinatorial optimization problem, the Traveling Salesman Problem, is evaluated on the basis of computational complexity measures and, subsequently, compared to performance of the Simultaneous Recurrent Neural network trained with the standard backpropagation, and recurrent backpropagation for the same static optimization problem. Simulation results indicate that the Simultaneous Recurrent Neural network trained with the resilient backpropagation algorithm is able to locate superior quality solutions through comparable amount of computational effort for the Traveling Salesman Problem.
THE ACCURATE ESTIMATION OF METEOROLOGICAL PROFILES EMPLOYING ANNs
Authors: TAMBOURATZIS TATIANA , GAZELA MYRSINI
Published: September 2002

The lack of meteorological measurements at a location of interest (target location) constitutes a problem that is crucial for the purposes of both weather forecasting and energy system design/validation. This paper constitutes a pilot study for the accurate estimation of meteorological values at a target location employing the meteorological measurements collected at a nearby (reference) location. Artificial neural networks are investigated and compared with traditional estimation methods such as linear models of first and higher orders and the non-linear model. The significance of the improvement obtained via the estimation — and especially the artificial neural network approach — over simply considering the measurements at the reference location is demonstrated in a number of energy applications.
A SELF-TUNING SOLUTION OF THE COSMOLOGICAL CONSTANT PROBLEM
Authors: KEHAGIAS A. , TAMVAKIS K.
Published: September 2002

We discuss the four-dimensional cosmological constant problem in a five-dimensional setting. A scalar field coupled to the SM forms dynamically a smooth brane with four-dimensional Poincaré invariance, independently of SM physics. In this respect, our solution may be regarded as a self-tuning solution, free of any singularities and fine-tuning problems.
ROBERTSON–SCHRÖDINGER INTELLIGENT STATES FOR TWO-BODY CALOGERO MODEL
Authors: DAOUD M.
Published: September 2002

Using the Gazeau–Klauder and Klauder–Perelomov coherent states, we derive the Robertson–Schrödinger intelligent states for two-body Calogero quantum system.