bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of the InvE Binding Site Required for Expression of IpaB of the
Shigella sonnei
Virulence Plasmid: Involvement of a ParB BoxA-Like Sequence
Authors: Taniya Takayuki , Mitobe Jiro , Nakayama Shu-ichi , Mingshan Qi , Okuda Kenji , Watanabe Haruo 
Published: August 2003

ABSTRACT

The InvE protein positively regulates the expression of virulence genes
ipaBCD
in
Shigella sonnei
. The InvE has significant homology with ParB of plasmid P1, which is known as a plasmid partitioning factor with DNA binding ability. Although the DNA binding activity of InvE has been predicted, it is not known whether the DNA binding activity is necessary for type III secretion system-associated gene expression. In this study, we determined the transcription start site of the
icsB-ipaBCD
operon (
ipa
operon) and constructed a series of deletions of the
icsB
promoter region in the
Escherichia coli
K-12 background. The deletion study revealed that an 86-bp region upstream of the
icsB
transcription start site was essential for expression of the
ipa
operon, where the ParB binding motif (ParB BoxA-like sequence) was observed. Purified glutathione
S
-transferase-InvE fusion protein bound directly to the −93 to −54 region (designating the
icsB
transcription start site as nucleotide +1) containing the ParB BoxA-like sequence. These results indicated that InvE bound directly to the promoter region.
Role of RopB in Growth Phase Expression of the SpeB Cysteine Protease ofStreptococcus pyogenes
Authors: Neely Melody N. , Lyon William R. , Runft Donna L. , Caparon Michael 
Published: August 2003

ABSTRACTThe Rgg family of transcription regulators is widely distributed among gram-positive bacteria; however, how the members of this family control transcription is poorly understood. In the pathogenStreptococcus pyogenes, the Rgg family member RopB is required for transcription of the gene that encodes the secreted SpeB cysteine protease. Expression of the protease follows distinct kinetics that involves control of transcription in response to the growth phase. In this study, the contribution of RopB to growth phase control was examined. The gene encoding the protease (speB) andropBare transcribed divergently from a 940-bp intergenic region. Primer extension analyses, in conjunction with reporter fusion studies, revealed that the major region controlling the transcription of bothspeBandropBis adjacent toropBand that the promoters for the two genes likely overlap. Furthermore, it was found that RopB is a DNA-binding protein that specifically binds to sequences in this control region. The interrelationship betweenropBandspeBexpression was further reflected in the observation that transcription ofropBitself is subject to growth phase control. However, while expression ofropBfrom a promoter expressed during the early logarithmic phase of growth could complement aropBdeletion mutant, ectopic expression ofropBdid not uncouple the expression ofspeBfrom its growth phase signal. These data implicate other factors in growth phase control and suggest that regulation ofropBexpression itself is not the central mechanism of control.
Characterization of an Exo-β-
d
-Glucosaminidase Involved in a Novel Chitinolytic Pathway from the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
KOD1
Authors: Tanaka Takeshi , Fukui Toshiaki , Atomi Haruyuki , Imanaka Tadayuki 
Published: August 2003

ABSTRACT

We previously clarified that the chitinase from the hyperthermophilic archaeon
Thermococcus kodakaraensis
KOD1 produces diacetylchitobiose (GlcNAc
2
) as an end product from chitin. Here we sought to identify enzymes in
T. kodakaraensis
that were involved in the further degradation of GlcNAc
2
. Through a search of the
T. kodakaraensis
genome, one candidate gene identified as a putative β-glycosyl hydrolase was found in the near vicinity of the chitinase gene. The primary structure of the candidate protein was homologous to the β-galactosidases in family 35 of glycosyl hydrolases at the N-terminal region, whereas the central region was homologous to β-galactosidases in family 42. The purified protein from recombinant
Escherichia coli
clearly showed an exo-β-
d
-glucosaminidase (GlcNase) activity but not β-galactosidase activity. This GlcNase (GlmA

Tk

), a homodimer of 90-kDa subunits, exhibited highest activity toward reduced chitobiose at pH 6.0 and 80°C and specifically cleaved the nonreducing terminal glycosidic bond of chitooligosaccharides. The GlcNase activity was also detected in
T. kodakaraensis
cells, and the expression of GlmA

Tk

was induced by GlcNAc
2
and chitin, strongly suggesting that GlmA

Tk

is involved in chitin catabolism in
T. kodakaraensis.
These results suggest that
T. kodakaraensis
, unlike other organisms, possesses a novel chitinolytic pathway where GlcNAc
2
from chitin is first deacetylated and successively hydrolyzed to glucosamine. This is the first report that reveals the primary structure of GlcNase not only from an archaeon but also from any organism.
The SopEΦ Phage Integrates into thessrAGeneof Salmonella entericaSerovar Typhimurium A36 and Is Closely Related to the Fels-2 Prophage
Authors: Pelludat Cosima , Mirold Susanne , Hardt Wolf-Dietrich 
Published: August 2003

ABSTRACTSalmonellaspp. are enteropathogenic gram-negative bacteria that use a large array of virulence factors to colonize the host, manipulate host cells, and resist the host's defense mechanisms. Even closely relatedSalmonellastrains have different repertoires of virulence factors. Bacteriophages contribute substantially to this diversity. There is increasing evidence that the reassortment of virulence factor repertoires by converting phages like the GIFSY phages and SopEΦ may represent an important mechanism in the adaptation ofSalmonellaspp. to specific hosts and to the emergence of new epidemic strains. Here, we have analyzed in more detail SopEΦ, a P2-like phage fromSalmonella entericaserovar Typhimurium DT204 that encodes the virulence factor SopE. We have cloned and characterized the attachment site (att) of SopEΦ and found that its 47-bp core sequence overlaps the 3′ terminus of thessrAgene of serovar Typhimurium. Furthermore, we have demonstrated integration of SopEΦ into the clonedattBsite of serovar Typhimurium A36. Sequence analysis of the plasmid-borne prophage revealed that SopEΦ is closely related to (60 to 100% identity over 80% of the genome) but clearly distinct from the Fels-2 prophage of serovar Typhimurium LT2 and from P2-like phages in the serovar Typhi CT18 genome. Our results demonstrate that there is considerable variation among the P2-like phages present in closely relatedSalmonellaspp.
Thin Pilus PilV Adhesins of Plasmid R64 Recognize Specific Structures of the Lipopolysaccharide Molecules of Recipient Cells
Authors: Ishiwa Akiko , Komano Teruya 
Published: August 2003

ABSTRACT

IncI1 plasmid R64 encodes a type IV pilus called a thin pilus, which includes PilV adhesins. Seven different sequences for the C-terminal segments of PilV adhesins can be produced by shufflon DNA rearrangement. The expression of the seven PilV adhesins determines the recipient specificity in liquid matings of plasmid R64.
Salmonella enterica
serovar Typhimurium LT2 was recognized by the PilVA′ and PilVB′ adhesins, while
Escherichia coli
K-12 was recognized by the PilVA′, PilVC, and PilVC′ adhesins. Lipopolysaccharide (LPS) on the surfaces of recipient cells was previously shown to be the specific receptor for the seven PilV adhesins. To identify the specific receptor structures of LPS for various PilV adhesins, R64 liquid matings were carried out with recipient cells consisting of various
S. enterica
serovar Typhimurium LT2 and
E. coli
K-12
waa
mutants and their derivatives carrying various
waa
genes of different origins. From the mating experiments, including inhibition experiments, we propose that the GlcNAc(α1-2)Glc and Glc(α1-2)Gal structures of the LPS core of
S. enterica
serovar Typhimurium LT2 function as receptors for the PilVB′ and PilVC′ adhesins, respectively, while the PilVC′ receptor in the wild-type LT2 LPS core may be masked. We further propose that the GlcNAc(β1-7)Hep and Glc(α1-2)Glc structures of the LPS core of
E. coli
K-12 function as receptors for the PilVC and PilVC′ adhesins, respectively.
Definition of a Second
Bacillus subtilis pur
Regulon Comprising the
pur
and
xpt-pbuX
Operons plus
pbuG
,
nupG
(
yxjA
), and
pbuE
(
ydhL
)
Authors: Johansen Lars Engholm , Nygaard Per , Lassen Catharina , Agersø Yvonne , Saxild Hans H. 
Published: August 2003

ABSTRACT

In
Bacillus subtilis
expression of genes or operons encoding enzymes and other proteins involved in purine synthesis is affected by purine bases and nucleosides in the growth medium. The genes belonging to the PurR regulon (
purR
,
purA
,
glyA
,
guaC
,
pbuO
,
pbuG
, and the
pur
,
yqhZ-folD
, and
xpt-pbuX
operons) are controlled by the PurR repressor, which inhibits transcription initiation. Other genes are regulated by a less-well-described transcription termination mechanism that responds to the presence of hypoxanthine and guanine. The
pur
operon and the
xpt-pbuX
operon, which were studied here, are regulated by both mechanisms. We isolated two mutants resistant to 2-fluoroadenine in which the
pur
operon and the
xpt-pbuX
operon are expressed at increased levels in a PurR-independent manner. The mutations were caused by deletions that disrupted a potential transcription terminator structure located immediately upstream of the
ydhL
gene. The 5′ part of the
ydhL
leader region contained a 63-nucleotide (nt) sequence very similar to the 5′ ends of the leaders of the
pur
and
xpt-pbuX
operons. Transcripts of these regions may form a common tandem stem-loop secondary structure. Two additional genes with potential leader regions containing the 63-nt sequence are
pbuG
, encoding a hypoxanthine-guanine transporter, and
yxjA
, which was shown to encode a purine nucleoside transporter and is renamed
nupG
. Transcriptional
lacZ
fusions and mutations in the 63-nt sequence encoding the possible secondary structures provided evidence that expression of the
pur
and
xpt-pbuX
operons and expression of the
ydhL
,
nupG
, and
pbuG
genes are regulated by a common mechanism. The new
pur
regulon is designated the XptR regulon. Except for
ydhL
, the operons and genes were negatively regulated by hypoxanthine and guanine.
ydhL
was positively regulated. The derived amino acid sequence encoded by
ydhL
(now called
pbuE
) is similar to the amino acid sequences of metabolite efflux pumps. When overexpressed, PbuE lowers the sensitivity to purine analogs. Indirect evidence indicated that PbuE decreases the size of the internal pool of hypoxanthine. This explains why the hypoxanthine- and guanine-regulated genes are expressed at elevated levels in a mutant that overexpresses
pbuE
.
Identification of a Differentially Expressed Oligopeptide Binding Protein (OppA2) in
Streptococcus uberis
by Representational Difference Analysis of cDNA
Authors: Taylor D. L. , Ward P. N. , Rapier C. D. , Leigh J. A. , Bowler L. D. 
Published: August 2003

ABSTRACT

Streptococcus uberis
is an increasingly significant cause of intramammary infection in the dairy cow, presently responsible for approximately 33% of all cases of bovine mastitis in the United Kingdom. Following experimentally induced infection of the lactating mammary gland,
S. uberis
is found predominantly in the luminal areas of secretory alveoli and ductular tissue, indicating that much of the bacterial growth occurs in residual and newly synthesized milk. With the objective of identifying potential virulence determinants in a clinical isolate of
S. uberis
, we have used representational difference analysis of cDNA to identify genes that show modified expression in milk. We have identified a number of differentially expressed genes that may contribute to the overall pathogenicity of the organism. Of these, a transcript encoding a putative oligopeptide binding protein (OppA) was further characterized. We have found that
S. uberis
possesses two
oppA
-like open reading frames,
oppA1
and
oppA2
, which are up-regulated to different degrees following growth in milk. Mutants lacking either
oppA1
or
oppA2
are viable and have an increased resistance to the toxic peptide derivative aminopterin; however, only mutants lacking
oppA1
display a lower rate of growth in milk. In addition, expression of the
oppA
genes appears to be coordinated by different mechanisms. We conclude that the
oppA
genes encode oligopeptide binding proteins, possibly displaying different specificities, required for the efficient growth of
S. uberis
in milk.
Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage
Authors: Miller Eric S. , Heidelberg John F. , Eisen Jonathan A. , Nelson William C. , Durkin A. Scott , Ciecko Ann , Feldblyum Tamara V. , White Owen , Paulsen Ian T. , Nierman William C. , Lee Jong , Szczypinski Bridget , Fraser Claire M. 
Published: August 2003

ABSTRACT

The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from
Vibrio
spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.
Topology of RbsC, the Membrane Component of the
Escherichia coli
Ribose Transporter
Authors: Stewart Jeffrey B. , Hermodson Mark A. 
Published: August 2003

ABSTRACT

The topology of RbsC, the membrane component of the ribose transporter in
Escherichia coli
, has been determined by using 34 single-cysteine mutants and a modified fluorescence labeling technique designated multiplex labeling. This technique gives topology, expression, and localization information for a membrane protein from a single batch of bacterial cells. The results indicate that RbsC contains 10 transmembrane-spanning helices, with the N and C termini being in the cytosol. This topology matches predictions from the latest prediction programs and the topology of the similar, recently crystallized membrane protein BtuC.
Yeast Two-Hybrid Studies on Interaction of Proteins Involved in Regulation of Nitrogen Fixation in the Phototrophic BacteriumRhodobacter capsulatus
Authors: Pawlowski Alice , Riedel Kai-Uwe , Klipp Werner , Dreiskemper Petra , Groß Silke , Bierhoff Holger , Drepper Thomas , Masepohl Bernd 
Published: August 2003

ABSTRACTRhodobacter capsulatuscontains two PII-like proteins, GlnB and GlnK, which play central roles in controlling the synthesis and activity of nitrogenase in response to ammonium availability. Here we used the yeast two-hybrid system to probe interactions between these PII-like proteins and proteins known to be involved in regulating nitrogen fixation. Analysis of defined protein pairs demonstrated the following interactions: GlnB-NtrB, GlnB-NifA1, GlnB-NifA2, GlnB-DraT, GlnK-NifA1, GlnK-NifA2, and GlnK-DraT. These results corroborate earlier genetic data and in addition show that PII-dependent ammonium regulation of nitrogen fixation inR. capsulatusdoes not require additional proteins, like NifL inKlebsiella pneumoniae. In addition, we found interactions for the protein pairs GlnB-GlnB, GlnB-GlnK, NifA1-NifA1, NifA2-NifA2, and NifA1-NifA2, suggesting that fine tuning of the nitrogen fixation process inR. capsulatusmay involve the formation of GlnB-GlnK heterotrimers as well as NifA1-NifA2 heterodimers. In order to identify new proteins that interact with GlnB and GlnK, we constructed anR. capsulatusgenomic library for use in yeast two-hybrid studies. Screening of this library identified the ATP-dependent helicase PcrA as a new putative protein that interacts with GlnB and the Ras-like protein Era as a new protein that interacts with GlnK.
The Genome Sequence of
Yersinia pestis
Bacteriophage φA1122 Reveals an Intimate History with the Coliphage T3 and T7 Genomes
Authors: Garcia Emilio , Elliott Jeffrey M. , Ramanculov Erlan , Chain Patrick S. G. , Chu May C. , Molineux Ian J. 
Published: August 2003

ABSTRACT

The genome sequence of bacteriophage φA1122 has been determined. φA1122 grows on almost all isolates of
Yersinia pestis
and is used by the Centers for Disease Control and Prevention as a diagnostic agent for the causative agent of plague. φA1122 is very closely related to coliphage T7; the two genomes are colinear, and the genome-wide level of nucleotide identity is about 89%. However, a quarter of the φA1122 genome, one that includes about half of the morphogenetic and maturation functions, is significantly more closely related to coliphage T3 than to T7. It is proposed that the yersiniophage φA1122 recombined with a close relative of the
Y. enterocolitica
phage φYeO3-12 to yield progeny phages, one of which became the classic T3 coliphage of Demerec and Fano (M. Demerec and U. Fano, Genetics
30:
119-136, 1945).
Cloning and Expression of the Gene for a Novel Protein from
Mycobacterium smegmatis
with Functional Similarity to Eukaryotic Calmodulin
Authors: Reddy Prasad T. , Prasad C. Rama , Reddy P. Hemalatha , Reeder Dennis , McKenney Keith , Jaffe Howard , Dimitrova Mariana N. , Ginsburg Ann , Peterkofsky Alan , Murthy P. Suryanarayana 
Published: August 2003

ABSTRACT

A calmodulin-like protein (CAMLP) from
Mycobacterium smegmatis
was purified to homogeneity and partially sequenced; these data were used to produce a full-length clone, whose DNA sequence contained a 55-amino-acid open reading frame.
M. smegmatis
CAMLP, expressed in
Escherichia coli
, exhibited properties characteristic of eukaryotic calmodulin: calcium-dependent stimulation of eukaryotic phosphodiesterase, which was inhibited by the calmodulin antagonist trifluoperazine, and reaction with anti-bovine brain calmodulin antibodies. Consistent with the presence of nine acidic amino acids (16%) in
M. smegmatis
CAMLP, there is one putative calcium-binding domain in this CAMLP, compared to four such domains for eukaryotic calmodulin, reflecting the smaller molecular size (approximately 6 kDa) of
M. smegmatis
CAMLP. Ultracentrifugation and mass spectral studies excluded the possibility that calcium promotes oligomerization of purified
M. smegmatis
CAMLP.
Complete Nucleotide Sequence and Genetic Organization of the 210-Kilobase Linear Plasmid ofRhodococcus erythropolisBD2
Authors: Stecker Christiane , Johann Andre , Herzberg Christina , Averhoff Beate , Gottschalk Gerhard 
Published: August 2003

ABSTRACTThe complete nucleotide sequence of the linear plasmid pBD2 fromRhodococcus erythropolisBD2 comprises 210,205 bp. Sequence analyses of pBD2 revealed 212 putative open reading frames (ORFs), 97 of which had an annotatable function. These ORFs could be assigned to six functional groups: plasmid replication and maintenance, transport and metalloresistance, catabolism, transposition, regulation, and protein modification. Many of the transposon-related sequences were found to flank the isopropylbenzene pathway genes. This finding together with the significant sequence similarities of theipbgenes to genes of the linear plasmid-encoded biphenyl pathway in other rhodococci suggests that theipbgenes were acquired via transposition events and subsequently distributed among the rhodococci via horizontal transfer.
Unique Degradation Signal for ClpCP inBacillus subtilis
Authors: Pan Qi , Losick Richard 
Published: August 2003

ABSTRACTRegulation of the cell-specific transcription factor σFin the spore-forming bacteriumBacillus subtilisinvolves the antisigma factor SpoIIAB. Contributing to the activation of σFis the degradation of SpoIIAB in a manner that depends on the protease ClpCP. Here we show that the three residues (LCN) located at the extreme C terminus of SpoIIAB are both necessary and sufficient for this degradation. We also report that the use of the LCN extension as a degradation signal for ClpCP is unique to SpoIIAB.
Polynucleotide Phosphorylase-Deficient Mutants ofPseudomonas putida
Authors: Favaro Rebecca , Dehò Gianni 
Published: August 2003

ABSTRACTIn bacteria, polynucleotide phosphorylase (PNPase) is one of the main exonucleolytic activities involved in RNA turnover and is widely conserved. In spite of this, PNPase does not seem to be essential for growth if the organisms are not subjected to special conditions, such as low temperature. We identified the PNPase-encoding gene (pnp) ofPseudomonas putidaand constructed deletion mutants that did not exhibit cold sensitivity. In addition, we found that the transcription pattern ofpnpupon cold shock inP. putidawas markedly different from that inEscherichia coli. It thus appears thatpnpexpression control and the physiological roles in the cold may be different in different bacterial species.
Efflux of Cytoplasmically Acting Antibiotics from Gram-Negative Bacteria: Periplasmic Substrate Capture by Multicomponent Efflux Pumps Inferred from Their Cooperative Action with Single-Component Transporters
Authors: Palmer Michael 
Published: August 2003

ABSTRACT
In gram-negative bacteria, coexpression of single- and multicomponent efflux pumps may result in multiplicative enhancement of the level of resistance against cytoplasmically acting antibiotics. Here, a simple model is presented to show that this cooperative effect can be accounted for only if substrate capture by the multicomponent efflux transporter occurs in the periplasm but not the cytosol.
Inactivation of
ompR
Promotes Precocious Swarming and
flhDC
Expression in
Xenorhabdus nematophila
Authors: Kim Dong-jin , Boylan Brian , George Nicholas , Forst Steven 
Published: August 2003

ABSTRACT

The response regulator OmpR is involved in numerous adaptive responses to environmental challenges. The role that OmpR plays in swarming behavior and swarm-cell differentiation in the symbiotic-pathogenic bacterium
Xenorhabdus nematophila
was examined in this study. Swarming began 4 h sooner in an
ompR
mutant strain than in wild-type cells. Precocious swarming was correlated with elevated expression of
fliC
, early flagellation, and cell elongation. The level of
flhDC
mRNA was elevated during the early period of swarming in the
ompR
strain relative to the level in the wild type. These findings show that OmpR is involved in the temporal regulation of
flhDC
expression and flagellum production and demonstrate that this response regulator plays a role in the swarming behavior of
X. nematophila
.