bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Analysis of Major Heat Shock Genes of
Helicobacter pylori
Authors: Homuth Georg , Domm Stephanie , Kleiner Diethelm , Schumann Wolfgang 
Published: July 2002

ABSTRACT

The transcriptional organization and heat inducibility of the major heat shock genes
hrcA
,
dnaK
,
dnaJ
,
groEL
, and
htpG
were analyzed on the transcriptional level in
Helicobacter pylori
strain 69A. The strongly heat-induced
dnaK
operon was found to be tricistronic, consisting of the genes
hrcA
,
grpE
, and
dnaK
. The
dnaJ
gene specified one monocistronic mRNA which was also heat inducible. The genes
groES
and
groEL
were transcribed as one strongly heat-inducible bicistronic mRNA which exhibited exactly the same induction kinetic as the
dnaK
operon. Surprisingly, transcription of the monocistronic
htpG
gene was switched off after heat shock. The data presented are discussed with regard to the different mechanisms regulating expression of heat shock genes in
H. pylori
Metabolic Instability of
Escherichia coli
Cyclopropane Fatty Acid Synthase Is Due to RpoH-Dependent Proteolysis
Authors: Chang Ying-Ying , Eichel Johannes , Cronan John E. 
Published: July 2002

ABSTRACT

Cyclopropane fatty acids (CFAs) are generally synthesized as bacterial cultures enter stationary phase. In
Escherichia coli
, the onset of CFA synthesis results from increased transcription of
cfa
, the gene encoding CFA synthase. However, the increased level of CFA synthase activity is transient; the activity quickly declines to the basal level. We report that the loss of CFA activity is due to proteolytic degradation dependent on expression of the heat shock regulon. CFA synthase degradation is unaffected by mutations in the
lon
,
clpP
, and
groEL
genes or by depletion of the intracellular ATP pools. It seems likely that CFA synthase is the target of an unidentified energy-independent heat shock regulon protease. This seems to be the first example of heat shock-dependent degradation of a normal biosynthetic enzyme.
Analysis of Nucleoid Morphology during Germination and Outgrowth of Spores ofBacillusSpecies
Authors: Ragkousi Katerina , Cowan Ann E. , Ross Margery A. , Setlow Peter 
Published: July 2002

ABSTRACTAfter a few minutes of germination, nucleoids in the great majority of spores ofBacillus subtilisandBacillus megateriumwere ring shaped. The major spore DNA binding proteins, the α/β-type small, acid-soluble proteins (SASP), colocalized to these nucleoid rings early in spore germination, as did theB. megateriumhomolog of the majorB. subtilischromosomal protein HBsu. The percentage of ring-shaped nucleoids was decreased in germinated spores with lower levels of α/β-type SASP. As spore outgrowth proceeded, the ring-shaped nucleoids disappeared and the nucleoid became more compact. This change took place after degradation of most of the spores' pool of major α/β-type SASP and was delayed when α/β-type SASP degradation was delayed. Later in spore outgrowth, the shape of the nucleoid reverted to the diffuse lobular shape seen in growing cells.
Action of the Thiamine Antagonist Bacimethrin on Thiamine Biosynthesis
Authors: Zilles Julie L. , Croal Laura R. , Downs Diana M. 
Published: July 2002

ABSTRACT

Bacimethrin is an analog of the 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) moiety of thiamine and inhibits the growth of
Salmonella enterica
serovar Typhimurium on a defined medium. Two classes of mutants that had increased bacimethrin resistance were isolated and characterized. Results showed that overexpression of the
thi
operon or specific lesions in
thiD
resulted in a bacimethrin-resistant phenotype. Phenotypic analyses of the
thiD
mutants suggested that they had a specific defect in one of the two kinase activities associated with this gene product and, further, that ThiD and not PdxK was primarily responsible for salvage of HMP from the medium.
FSY1
, a Novel Gene Encoding a Specific Fructose/H
+
Symporter in the Type Strain of
Saccharomyces carlsbergensis
Authors: Gonçalves Paula , Rodrigues de Sousa Helena , Spencer-Martins Isabel 
Published: July 2002

ABSTRACT

A novel gene,
FSY1
, encoding a permease involved in active fructose uptake by a proton symport mechanism in the type strain of
Saccharomyces carlsbergensis
has been isolated. Fsy1p is only distantly related to the Hxt proteins that mediate facilitated diffusion of glucose and fructose in
Saccharomyces cerevisiae
and related species.
Expression of
cbsA
Encoding the Collagen-Binding S-Protein of
Lactobacillus crispatus
JCM5810 in
Lactobacillus casei
ATCC 393
T
Authors: Martı́nez Beatriz , Sillanpää Jouko , Smit Egbert , Korhonen Timo K. , Pouwels Peter H. 
Published: July 2002

ABSTRACT

The
cbsA
gene encoding the collagen-binding S-layer protein of
Lactobacillus crispatus
JCM5810 was expressed in
L. casei
ATCC 393
T
. The S-protein was not retained on the surface of the recombinant bacteria but was secreted into the medium. By translational fusion of CbsA to the cell wall sorting signal of the proteinase, PrtP, of
L. casei
, CbsA was presented at the surface, rendering the transformants able to bind to immobilized collagens.
Cloning and Characterization of Sialidases with 2-6′ and 2-3′ Sialyl Lactose Specificity from
Pasteurella multocida
Authors: Mizan Shaikh , Henk Adam , Stallings Amy , Maier Marie , Lee Margie D. 
Published: July 2002

ABSTRACT

Pasteurella multocida
is a mucosal pathogen that colonizes the respiratory system of susceptible hosts. Most isolates of
P. multocida
produce sialidase activity, which may contribute to colonization of the respiratory tract or the production of lesions in an active infection. We have cloned and sequenced a sialidase gene,
nanH
, from a fowl cholera isolate of
P. multocida
. Sequence analysis of NanH revealed that it exhibited significant amino acid sequence homology with many microbial sialidases. Insertional inactivation of
nanH
resulted in a mutant strain that was not deficient in sialidase production. However, this mutant exhibited reduced enzyme activity and growth rate on 2-3′ sialyl lactose compared to the wild type. Subsequently, we demonstrated the presence of two sialidases by cloning another sialidase gene that differed from
nanH
in DNA sequence and substrate specificity. NanB demonstrated activity on both 2-3′ and 2-6′ sialyl lactose, while NanH demonstrated activity only on 2-3′ sialyl lactose. Neither enzyme liberated sialic acid from colominic acid (2-8′ sialyl lactose). Recombinant
E. coli
containing the sialidase genes were able to utilize several sialoconjugants when they were provided as sole carbon sources in minimal medium. These data suggest that sialidases have a nutritional function and may contribute to the ability of
P. multocida
to colonize and persist on vertebrate mucosal surfaces.
Pleiotropic Effect of Protein P6 on the Viral Cycle of Bacteriophage φ29
Authors: Camacho Ana , Salas Margarita 
Published: July 2002

ABSTRACT

The product of bacteriophage φ29 early gene 6, protein p6, is a double-stranded-DNA binding protein and one of the more abundant proteins during viral infection. We have studied the role of protein p6 in vivo through the infection of suppressor and nonsuppressor
Bacillus subtilis
strains with a phage carrying a nonsense mutation in gene 6, sus6(626). In the absence of functional protein p6, the two major processes of the viral cycle, transcription and DNA replication, were affected. Viral DNA synthesis was practically abolished, and early transcription was remarkably delayed and, in addition, underregulated at late times of the infection. The amount of protein p6 synthesized after infection with mutant phage sus6(626) under suppressor conditions was sixfold lower than that produced after wild-type infection. Nonetheless, phage production was as high as that obtained after wild-type infection. These results indicate that p6 is synthesized in amounts higher than those needed for most of its functions. However, the concentration of protein p6 appeared to be important for repression of the early promoter C2.
Cloning and Characterization of the
Flavobacterium johnsoniae
Gliding-Motility Genes
gldB
and
gldC
Authors: Hunnicutt David W. , McBride Mark J. 
Published: July 2002

ABSTRACT

The mechanism of bacterial gliding motility (active movement over surfaces without the aid of flagella) is not known. A large number of mutants of the gliding bacterium
Flavobacterium johnsoniae
(
Cytophaga johnsonae
) with defects in gliding motility have been previously isolated, and genetic techniques to analyze these mutants have recently been developed. We complemented a nongliding mutant of
F. johnsoniae
(UW102-99) with a library of wild-type DNA by using the shuttle cosmid pCP26. The complementing plasmid (pCP200) contained an insert of 26 kb and restored gliding motility to 4 of 50 independently isolated nongliding mutants. A 1.9-kb fragment which encompassed two genes,
gldB
and
gldC
, complemented all four mutants. An insertion mutation in
gldB
was polar on
gldC
, suggesting that the two genes form an operon. Disruption of the chromosomal copy of
gldB
in wild-type
F. johnsoniae
UW101 eliminated gliding motility. Introduction of the
gldBC
operon, or
gldB
alone, restored motility.
gldB
appears to be essential for
F. johnsoniae
gliding motility. It codes for a membrane protein that does not exhibit strong sequence similarity to other proteins in the databases.
gldC
is not absolutely required for gliding motility, but cells that do not produce GldC form colonies that spread less well than those of the wild type. GldC is a soluble protein and has weak sequence similarity to the fungal lectin AOL.
Identification of a Chitin-Binding Protein Secreted by
Pseudomonas aeruginosa
Authors: Folders Jindra , Tommassen Jan , van Loon Leendert C. , Bitter Wilbert 
Published: July 2002

ABSTRACT

One of the major proteins secreted by
Pseudomonas aeruginosa
is a 43-kDa protein, which is cleaved by elastase into smaller fragments, including a 30-kDa and a 23-kDa fragment. The N-terminal 23-kDa fragment was previously suggested as corresponding to a staphylolytic protease and was designated LasD (S. Park and D. R. Galloway, Mol. Microbiol. 16:263–270, 1995). However, the sequence of the gene encoding this 43-kDa protein revealed that the N-terminal half of the protein is homologous to the chitin-binding proteins CHB1 of
Streptomyces olivaceoviridis
and CBP21 of
Serratia marcescens
and to the cellulose-binding protein p40 of
Streptomyces halstedii
. Furthermore, a short C-terminal fragment shows homology to a part of chitinase A of
Vibrio harveyi
. The full-length 43-kDa protein could bind chitin and was thereby protected against the proteolytic activity of elastase, whereas the degradation products did not bind chitin. The purified 43-kDa chitin-binding protein had no staphylolytic activity, and comparison of the enzymatic activities in the extracellular medium of a wild-type strain and a chitin-binding protein-deficient mutant indicated that the 43-kDa protein supports neither chitinolytic nor staphylolytic activity. We conclude that the 43-kDa protein, which was found to be produced by many clinical isolates of
P. aeruginosa
, is a chitin-binding protein, and we propose to name it CbpD (chitin-binding protein D).
Partitioning of the Linear Chromosome during Sporulation of
Streptomyces coelicolor
A3(2) Involves an
oriC
-Linked
parAB
Locus
Authors: Kim Hyun-Jin , Calcutt Michael J. , Schmidt Francis J. , Chater Keith F. 
Published: July 2002

ABSTRACT

Candidate partitioning genes (
parA
and
parB
) for the linear chromosome of
Streptomyces coelicolor
were identified by DNA sequencing in a series of seven genes located between
rnpA
and
trxA
near the chromosomal replication origin. The most likely translation start point of
parB
overlapped the
parA
stop codon, suggestive of coregulation, and transcription analysis suggested that the two genes formed an operon. Deletion of part of
parB
had no effect on the growth or appearance of colonies but caused a deficiency in DNA partitioning during the multiple septation events involved in converting aerial hyphae into long chains of spores. At least 13% of spore compartments failed to inherit the normal DNA allocation. The same phenotype was obtained with a deletion removing a segment of DNA from both
parA
and
parB
. Reinforcing the idea of a special role for the
par
locus during sporulation, the stronger of two
parAB
promoters was greatly upregulated at about the time when sporulation septation was maximal in colonies. Three copies of a 14-bp inverted repeat (GTTTCACGTGAAAC) were found in or near the
parAB
genes, and at least 12 more identical copies were identified within 100 kb of
oriC
from the growing genome sequence database. Only one perfect copy of the 14-bp sequence was present in approximately 5 Mb of sequence available from the rest of the genome. The 14-bp sequence was similar to sequences identified as binding sites for Spo0J, a ParB homologue from
Bacillus subtilis
believed to be important for DNA partitioning (D. C.-H. Lin and A. D. Grossman, Cell 92:675–685, 1998). One of these sites encompassed the transcription start point of the stronger
parA
promoter.
Penicillin-Binding Protein-Related Factor A Is Required for Proper Chromosome Segregation in
Bacillus subtilis
Authors: Pedersen Lotte B. , Setlow Peter 
Published: July 2002

ABSTRACT

Previous work has shown that the
ponA
gene, encoding penicillin-binding protein 1 (PBP1), is in a two-gene operon with
prfA
(PBP-related factor A) (also called
recU
), which encodes a putative 206-residue basic protein (pI = 10.1) with no significant sequence homology to proteins with known functions. Inactivation of
prfA
results in cells that grow slower and vary significantly in length relative to wild-type cells. We now show that
prfA
mutant cells have a defect in chromosome segregation resulting in the production of ∼0.9 to 3% anucleate cells in
prfA
cultures grown at 30 or 37°C in rich medium and that the lack of PrfA exacerbates the chromosome segregation defect in
smc
and
spoOJ
mutant cells. In addition, overexpression of
prfA
was found to be toxic for and cause nucleoid condensation in
Escherichia coli.
Structural and Functional Analysis of the Phosphonoacetate Hydrolase (
phnA
) Gene Region in
Pseudomonas fluorescens
23F
Authors: Kulakova Anna N. , Kulakov Leonid A. , Akulenko Natalya V. , Ksenzenko Vladimir N. , Hamilton John T. G. , Quinn John P. 
Published: July 2002

ABSTRACT

The
Pseudomonas fluorescens
23F phosphonoacetate hydrolase gene (
phnA
) encodes a novel carbon-phosphorus bond cleavage enzyme whose expression is independent of the phosphate status of the cell. Analysis of the regions adjacent to the phosphonoacetate hydrolase structural gene (
phnA
) indicated the presence of five open reading frames (ORFs). These include one (
phnR
) whose putative product shows high levels of homology to the LysR family of positive transcriptional regulators. Its presence was shown to be necessary for induction of the hydrolase activity. 2-Phosphonopropionate was found to be an inducer (and poor substrate) for phosphonoacetate hydrolase. Unlike phosphonoacetate, which is also an inducer of phosphonoacetate hydrolase, entry of 2-phosphonopropionate into cells appeared to be dependent on the presence of a gene (
phnB
) that lies immediately downstream of
phnA
and whose putative product shows homology to the glycerol-3-phosphate transporter. RNA analysis revealed transcripts for the
phnAB
and
phnR
operons, which are transcribed divergently; the resulting mRNAs overlapped by 29 nucleotide bases at their 5′ ends. Transcripts of
phnAB
were detected only in cells grown in the presence of phosphonoacetate, whereas transcripts of
phnR
were observed in cells grown under both induced and uninduced conditions. The expression of three additional genes found in the
phnA
region did not appear necessary for the degradation of phosphonoacetate and 2-phosphonopropionate by either
Pseudomonas putida
or
Escherichia coli
cells.
Red Fluorescent Protein (DsRed) as a Reporter in
Saccharomyces cerevisiae
Authors: Rodrigues Fernando , van Hemert Martijn , Steensma H. Yde , Côrte-Real Manuela , Leão Cecı́la 
Published: July 2002

ABSTRACT

We describe the utilization of a red fluorescent protein (DsRed) as an in vivo marker for
Saccharomyces cerevisiae
. Clones expressing red and/or green fluorescent proteins with both cytoplasmic and nuclear localization were obtained. A series of vectors are now available which can be used to create amino-terminal (N-terminal) and carboxyl-terminal (C-terminal) fusions with the DsRed protein.
Overexpression of the MexEF-OprN Multidrug Efflux System Affects Cell-to-Cell Signaling in
Pseudomonas aeruginosa
Authors: Köhler Thilo , van Delden Christian , Curty Lasta Kocjancic , Hamzehpour Mehri Michea , Pechere Jean-Claude 
Published: July 2002

ABSTRACT

Intrinsic and acquired antibiotic resistance of the nosocomial pathogen
Pseudomonas aeruginosa
is mediated mainly by the expression of several efflux pumps of broad substrate specificity. Here we report that
nfxC
type mutants, overexpressing the MexEF-OprN efflux system, produce lower levels of extracellular virulence factors than the susceptible wild type. These include pyocyanin, elastase, and rhamnolipids, three factors controlled by the
las
and
rhl
quorum-sensing systems of
P. aeruginosa
. In agreement with these observations are the decreased transcription of the elastase gene
lasB
and the rhamnosyltransferase genes
rhlAB
measured in
nfxC
type mutants. Expression of the
lasR
and
rhlR
regulator genes was not affected in the
nfxC
type mutant. In contrast, transcription of the C4-homoserine lactone (C4-HSL) autoinducer synthase gene
rhlI
was reduced by 50% in the
nfxC
type mutant relative to that in the wild type. This correlates with a similar decrease in C4-HSL levels detected in supernatants of the
nfxC
type mutant. Transcription of an
rhlAB
-
lacZ
fusion could be partially restored by the addition of synthetic C4-HSL and
Pseudomonas
quinolone signal (PQS). It is proposed that the MexEF-OprN efflux pump affects intracellular PQS levels.
The
djlA
Gene Acts Synergistically with
dnaJ
in Promoting
Escherichia coli
Growth
Authors: Genevaux Pierre , Schwager Françoise , Georgopoulos Costa , Kelley William L. 
Published: July 2002

ABSTRACT

The DnaK chaperone of
Escherichia coli
is known to interact with the J domains of DnaJ, CbpA, and DjlA. By constructing multiple mutants, we found that the
djlA
gene was essential for bacterial growth above 37°C in the absence of
dnaJ
. This essentiality depended upon the J domain of DjlA but not upon the normal membrane location of DjlA.
Genetic Locus Required for Antigenic Maturation of
Rhizobium etli
CE3 Lipopolysaccharide
Authors: Duelli Dominik M. , Tobin Andrea , Box Jodie M. , Kolli V. S. Kumar , Carlson Russell W. , Noel K. Dale 
Published: July 2002

ABSTRACT

Rhizobium etli
modifies lipopolysaccharide (LPS) structure in response to environmental signals, such as low pH and anthocyanins. These LPS modifications result in the loss of reactivity with certain monoclonal antibodies. The same antibodies fail to recognize previously isolated
R. etli
mutant strain CE367, even in the absence of such environmental cues. Chemical analysis of the LPS in strain CE367 demonstrated that it lacked the terminal sugar of the wild-type O antigen, 2,3,4-tri-
O
-methylfucose. A 3-kb stretch of DNA, designated as
lpe3
, restored wild-type antigenicity when transferred into CE367. From the sequence of this DNA, five open reading frames were postulated. Site-directed mutagenesis and complementation analysis suggested that the genes were organized in at least two transcriptional units, both of which were required for the production of LPS reactive with the diagnostic antibodies. Growth in anthocyanins or at low pH did not alter the specific expression of
gusA
from the transposon insertion of mutant CE367, nor did the presence of multiple copies of
lpe3
situated behind a strong, constitutive promoter prevent epitope changes induced by these environmental cues. Mutations of the
lpe
genes did not prevent normal nodule development on
Phaseolus vulgaris
and had very little effect on the occupation of nodules in competition with the wild-type strain.
Global Transcriptional Response of
Bacillus subtilis
to Heat Shock
Authors: Helmann John D. , Wu Ming Fang Winston , Kobel Phil A. , Gamo Francisco-Javier , Wilson Michael , Morshedi Maud M. , Navre Marc , Paddon Chris 
Published: July 2002

ABSTRACT

In response to heat stress,
Bacillus subtilis
activates the transcription of well over 100 different genes. Many of these genes are members of a general stress response regulon controlled by the secondary sigma factor, ς
B
, while others are under control of the HrcA or CtsR heat shock regulators. We have used DNA microarrays to monitor the global transcriptional response to heat shock. We find strong induction of known ς
B
-dependent genes with a characteristic rapid induction followed by a return to near prestimulus levels. The HrcA and CtsR regulons are also induced, but with somewhat slower kinetics. Analysis of DNA sequences proximal to newly identified heat-induced genes leads us to propose ∼70 additional members of the ς
B
regulon. We have also identified numerous heat-induced genes that are not members of known heat shock regulons. Notably, we observe very strong induction of arginine biosynthesis and transport operons. Induction of several genes was confirmed by quantitative reverse transcriptase PCR. In addition, the transcriptional responses measured by microarray hybridization compare favorably with the numerous previous studies of heat shock in this organism. Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses.
Cytoplasmic Filament-Deficient Mutant of
Treponema denticola
Has Pleiotropic Defects
Authors: Izard Jacques , Samsonoff William A. , Limberger Ronald J. 
Published: July 2002

ABSTRACT

In
Treponema denticola
, a ribbon-like structure of cytoplasmic filaments spans the cytoplasm at all stages of the cell division process. Insertional inactivation was used as a first step to determine the function of the cytoplasmic filaments. A suicide plasmid was constructed that contained part of
cfpA
and a nonpolar erythromycin resistance cassette (
ermF
and
ermAM
) inserted near the beginning of the gene. The plasmid was electroporated into
T. denticola
, and double-crossover recombinants which had the chromosomal copy of
cfpA
insertionally inactivated were selected. Immunoblotting and electron microscopy confirmed the lack of cytoplasmic filaments. The mutant was further analyzed by dark-field microscopy to determine cell morphology and by the binding of two fluorescent dyes to DNA to assess the distribution of cellular nucleic acids. The cytoplasmic filament protein-deficient mutant exhibited pleiotropic defects, including highly condensed chromosomal DNA, compared to the homogeneous distribution of the DNA throughout the cytoplasm in a wild-type cell. Moreover, chains of cells are formed by the cytoplasmic filament-deficient mutant, and those cells show reduced spreading in agarose, which may be due to the abnormal cell length. The chains of cells and the highly condensed chromosomal DNA suggest that the cytoplasmic filaments may be involved in chromosome structure, segregation, or the cell division process in
Treponema
.