bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Expression of the 2-Deoxy-
d
-Ribose Utilization Regulon,
deoQKPX
, from
Salmonella enterica
Serovar Typhimurium
Authors: Christensen Mette , Borza Tudor , Dandanell Gert , Gilles Anne-Marie , Barzu Octavian , Kelln Rod A. , Neuhard Jan 
Published: October 2003

ABSTRACT

Salmonella enterica
, in contrast to
Escherichia coli
K12, can use 2-deoxy-
d
-ribose as the sole carbon source. The genetic determinants for this capacity in
S. enterica
serovar Typhimurium include four genes, of which three,
deoK
,
deoP
, and
deoX
, constitute an operon. The fourth,
deoQ
, is transcribed in the opposite direction. The
deoK
gene encodes deoxyribokinase. In silico analyses indicated that
deoP
encodes a permease and
deoQ
encodes a regulatory protein of the
deoR
family. The
deoX
gene product showed no match to known proteins in the databases. Deletion analyses showed that both a functional
deoP
gene and a functional
deoX
gene were required for optimal utilization of deoxyribose. Using gene fusion technology, we observed that
deoQ
and the
deoKPX
operon were transcribed from divergent promoters located in the 324-bp intercistronic region between
deoQ
and
deoK
. The
deoKPX
promoter was 10-fold stronger than the
deoQ
promoter, and expression was negatively regulated by DeoQ as well as by DeoR, the repressor of the deoxynucleoside catabolism operon. Transcription of
deoKPX
but not of
deoQ
was regulated by catabolite repression. Primer extension analysis identified the transcriptional start points of both promoters and showed that induction by deoxyribose occurred at the level of transcription initiation. Gel retardation experiments with purified DeoQ illustrated that it binds independently to tandem operator sites within the
deoQ
and
deoK
promoter regions with

K
d

values of 54 and 2.4 nM, respectively.
A Second PDZ-Containing Serine Protease Contributes to Activation of the Sporulation Transcription Factor σKinBacillus subtilis
Authors: Pan Qi , Losick Richard , Rudner David Z. 
Published: October 2003

ABSTRACTGene expression late during the process of sporulation inBacillus subtilisis governed by a multistep, signal transduction pathway involving the transcription factor σK, which is derived by regulated proteolysis from the inactive proprotein pro-σK. Processing of pro-σKis triggered by a signaling protein known as SpoIVB, a serine protease that contains a region with similarity to the PDZ family of protein-protein interaction domains. Here we report the discovery of a second PDZ-containing serine protease called CtpB that contributes to the activation of the pro-σKprocessing pathway. CtpB is a sporulation-specific, carboxyl-terminal processing protease and shares several features with SpoIVB. We propose that CtpB acts to fine-tune the regulation of pro-σKprocessing, and we discuss possible models by which CtpB influences the σKactivation pathway.
Positive Correlation between Tyrosine Phosphorylation of CpsD and Capsular Polysaccharide Production inStreptococcus pneumoniae
Authors: Bender Matthew H. , Cartee Robert T. , Yother Janet 
Published: October 2003

ABSTRACTCpsA, CpsB, CpsC, and CpsD are part of a tyrosine phosphorylation regulatory system involved in modulation of capsule synthesis inStreptococcus pneumoniaeand many other gram-positive and gram-negative bacteria. Using an immunoblotting technique, we observed distinct laddering patterns ofS. pneumoniaecapsular polysaccharides of various serotypes and found that transfer of the polymer from the membrane to the cell wall was independent of size. Deletion ofcps2A,cps2B,cps2C, orcps2Din the serotype 2 strain D39 did not affect the ability to transfer capsule to the cell wall. Deletion ofcps2Corcps2D, which encode two domains of an autophosphorylating tyrosine kinase, resulted in the production of only short-chain polymers. The function of Cps2A is unknown, and the polymer laddering pattern of thecps2Adeletion mutants appeared similar to that of the parent, although the total amount of capsule was decreased. Loss of Cps2B, a tyrosine phosphatase and a kinase inhibitor, resulted in an increase in capsule amount and a normal ladder pattern. However, Cps2B mutants exhibited reduced virulence following intravenous inoculation of mice and were unable to colonize the nasopharynx, suggesting a diminished capacity to sense or respond to these environments. In D39 and its isogenic mutants, the amounts of capsule and tyrosine-phosphorylated Cps2D (Cps2D∼P) correlated directly. In contrast, restoration of type 2 capsule production followed by deletion ofcps2Bin Rx1, a laboratory passaged D39 derivative containing multiple uncharacterized mutations, resulted in decreased capsule amounts but no alteration in Cps2D∼P levels. Thus, a factor outside the capsule locus, which is either missing or defective in the Rx1 background, is important in the control of capsule synthesis.
Regulation of Expression of Cellulosomal Cellulase and Hemicellulase Genes in
Clostridium cellulovorans
Authors: Han Sung Ok , Yukawa Hideaki , Inui Masayuki , Doi Roy H. 
Published: October 2003

ABSTRACT

The regulation of expression of the genes encoding the cellulases and hemicellulases of
Clostridium cellulovorans
was studied at the mRNA level with cells grown under various culture conditions. A basic pattern of gene expression and of relative expression levels was obtained from cells grown in media containing poly-, di- or monomeric sugars. The cellulase (
cbpA
and
engE
) and hemicellulase (
xynA
) genes were coordinately expressed in medium containing cellobiose or cellulose. Growth in the presence of cellulose, xylan, and pectin gave rise to abundant expression of most genes (
cbpA
-
exgS
,
engH
,
hbpA
,
manA
,
engM
,
engE
,
xynA
, and/or
pelA
) studied. Moderate expression of
cbpA
,
engH
,
manA
,
engE
, and
xynA
was observed when cellobiose or fructose was used as the carbon source. Low levels of mRNA from
cbpA
,
manA
,
engE
, and
xynA
were observed with cells grown in lactose, mannose, and locust bean gum, and very little or no expression of
cbpA
,
engH
,
manA
,
engE
, and
xynA
was detected in glucose-, galactose-, maltose-, and sucrose-grown cells. The
cbpA
-
exgS
and
engE
genes were most frequently expressed under all conditions studied, whereas expression of
xynA
and
pelA
was more specifically induced at higher levels in xylan- or pectin-containing medium, respectively. Expression of the genes (
cbpA
,
hbpA
,
manA
,
engM
, and
engE
) was not observed in the presence of most soluble di- or monosaccharides such as glucose. These results support the hypotheses that there is coordinate expression of some cellulases and hemicellulases, that a catabolite repression type of mechanism regulates cellulase expression in rapidly growing cells, and that the presence of hemicelluloses has an effect on cellulose utilization by the cell.
Global Mutational Analysis of NtrC-Like Activators in
Myxococcus xanthus
: Identifying Activator Mutants Defective for Motility and Fruiting Body Development
Authors: Caberoy Nora B. , Welch Roy D. , Jakobsen Jimmy S. , Slater Steven C. , Garza Anthony G. 
Published: October 2003

ABSTRACT

The multicellular developmental cycle of
Myxococcus xanthus
requires large-scale changes in gene transcription, and recent findings indicate that NtrC-like activators play a prominent role in regulating these changes. In this study, we made insertions in 28 uncharacterized
ntrC
-like activator (
nla
) genes and found that eight of these insertions cause developmental defects. Hence, these results are consistent with the idea that
M. xanthus
uses a series of different NtrC-like activators during fruiting body development. Four of the eight developmental mutants we identified have motility defects. The
nla1
,
nla19
, and
nla23
mutants show S-motility defects, while the
nla24
mutant shows defects in both S-motility and A-motility. During development, aggregation of the
nla1
,
nla19
, and
nla23
mutants is delayed slightly and the
nla24
mutant shows no signs of aggregation or sporulation. The
nla4
,
nla6
,
nla18
, and
nla28
mutants have no appreciable loss in motility, but they fail to aggregate and to sporulate normally. The
nla18
mutant belongs to a special class of developmental mutants whose defects can be rescued when they are codeveloped with wild-type cells, suggesting that
nla18
fails to produce a cell-cell signal required for development. The three remaining activator mutants,
nla4
,
nla6
, and
nla28
, appear to have complex developmental phenotypes that include deficiencies in cell-cell developmental signals.
Cryo-Transmission Electron Microscopy of Frozen-Hydrated Sections ofEscherichia coliandPseudomonas aeruginosa
Authors: Matias Valério R. F. , Al-Amoudi Ashraf , Dubochet Jacques , Beveridge Terry J. 
Published: October 2003

ABSTRACTHigh-pressure freezing ofEscherichia coliK-12 andPseudomonas aeruginosaPAO1 in the presence of cryoprotectants provided consistent vitrification of cells so that frozen-hydrated sections could be cut, providing ∼2-nm resolution of structure. The size and shape of the bacteria, as well as their surface and cytoplasmic constituents, were nicely preserved and compared well with other published high-resolution techniques. Cells possessed a rich cytoplasm containing a diffuse dispersion of ribosomes and genetic material. Close examination of cells revealed that the periplasmic space was compressed during cryosectioning, a finding which provided supporting evidence that this space is filled by a compressible gel. Since the outer membrane and peptidoglycan layer are bonded together via lipoproteins, the space between them (although still part of the periplasmic space) was not as compacted. Even when this cryosectioning compression was taken into account, there was still substantial variability in the width of the periplasmic space. It is possible that the protoplast has some capacity to float freely within the periplasm.
2-Oxoglutarate:NADP
+
Oxidoreductase in
Azoarcus evansii
: Properties and Function in Electron Transfer Reactions in Aromatic Ring Reduction
Authors: Ebenau-Jehle Christa , Boll Matthias , Fuchs Georg 
Published: October 2003

ABSTRACT

The conversion of [
14
C]benzoyl-coenzyme A (CoA) to nonaromatic products in the denitrifying β-proteobacterium
Azoarcus evansii
grown anaerobically on benzoate was investigated. With cell extracts and 2-oxoglutarate as the electron donor, benzoyl-CoA reduction occurred at a rate of 10 to 15 nmol min
−1
mg
−1
. 2-Oxoglutarate could be replaced by dithionite (200% rate) and by NADPH (∼10% rate); in contrast NADH did not serve as an electron donor. Anaerobic growth on aromatic compounds induced 2-oxoglutarate:acceptor oxidoreductase (KGOR), which specifically reduced NADP
+
, and NADPH:acceptor oxidoreductase. KGOR was purified by a 76-fold enrichment. The enzyme had a molecular mass of 290 ± 20 kDa and was composed of three subunits of 63 (γ), 62 (α), and 37 (β) kDa in a 1:1:1 ratio, suggesting an (αβγ)
2
composition. The native enzyme contained Fe (24 mol/mol of enzyme), S (23 mol/mol), flavin adenine dinucleotide (FAD; 1.4 mol/mol), and thiamine diphosphate (0.95 mol/mol). KGOR from
A. evansii
was highly specific for 2-oxoglutarate as the electron donor and accepted both NADP
+
and oxidized viologens as electron acceptors; in contrast NAD
+
was not reduced. These results suggest that benzoyl-CoA reduction is coupled to the complete oxidation of the intermediate acetyl-CoA in the tricarboxylic acid cycle. Electrons generated by KGOR can be transferred to both oxidized ferredoxin and NADP
+
, depending on the cellular needs. N-terminal amino acid sequence analysis revealed that the open reading frames for the three subunits of KGOR are similar to three adjacently located open reading frames in
Bradyrhizobium japonicum
. We suggest that these genes code for a very similar three-subunit KGOR, which may play a role in nitrogen fixation. The α-subunit is supposed to harbor one FAD molecule, two [4Fe-4S] clusters, and the NADPH binding site; the β-subunit is supposed to harbor one thiamine diphosphate molecule and one further [4Fe-4S] cluster; and the γ-subunit is supposed to harbor the CoA binding site. This is the first study of an NADP
+
-specific KGOR. A similar NADP
+
-specific pyruvate oxidoreductase, which contains all domains in one large subunit, has been reported for the mitochondrion of the protist
Euglena gracilis
and the apicomplexan
Cryptosporidium parvum
.
Molecular Characterization of
Brucella abortus
Chromosome II Recombination
Authors: Tsoktouridis Georgios , Merz Christian A. , Manning Simon P. , Giovagnoli-Kurtz Renée , Williams Leanne E. , Mujer Cesar V. , Hagius Sue , Elzer Philip , Redkar Rajendra J. , Patra Guy , DelVecchio Vito G. 
Published: October 2003

ABSTRACT

Large-scale genomic rearrangements including inversions, deletions, and duplications are significant in bacterial evolution. The recently completed
Brucella melitensis
16M and
Brucella suis
1330 genomes have facilitated the investigation of such events in the
Brucella
spp. Suppressive subtractive hybridization (SSH) was employed in identifying genomic differences between
B. melitensis
16M and
Brucella abortus
2308. Analysis of 45 SSH clones revealed several deletions on chromosomes of
B. abortus
and
B. melitensis
that encoded proteins of various metabolic pathways. A 640-kb inversion on chromosome II of
B. abortus
has been reported previously (S. Michaux Charachon, G. Bourg, E. Jumas Bilak, P. Guigue Talet, A. Allardet Servent, D. O'Callaghan, and M. Ramuz, J. Bacteriol.
179:
3244-3249, 1997) and is further described in this study. One end of the inverted region is located on a deleted TATGC site between open reading frames BMEII0292 and BMEII0293. The other end inserted at a GTGTC site of the cyclic-di-GMP phosphodiesterase A (PDEA) gene (BMEII1009), dividing PDEA into two unequal DNA segments of 160 and 977 bp. As a consequence of inversion, the 160-bp segment that encodes the N-terminal region of PDEA was relocated at the opposite end of the inverted chromosomal region. The splitting of the PDEA gene most likely inactivated the function of this enzyme. A recombination mechanism responsible for this inversion is proposed.
ATP-Bound Conformation of Topoisomerase IV: a Possible Target for Quinolones in
Streptococcus pneumoniae
Authors: Sifaoui Farid , Lamour Valérie , Varon Emmanuelle , Moras Dino , Gutmann Laurent 
Published: October 2003

ABSTRACT

Topoisomerase IV, a C
2
E
2
tetramer, is involved in the topological changes of DNA during replication. This enzyme is the target of antibacterial compounds, such as the coumarins, which target the ATP binding site in the ParE subunit, and the quinolones, which bind, outside the active site, to the quinolone resistance-determining region (QRDR). After site-directed and random mutagenesis, we found some mutations in the ATP binding site of ParE near the dimeric interface and outside the QRDR that conferred quinolone resistance to
Streptococcus pneumoniae
, a bacterial pathogen. Modeling of the N-terminal, 43-kDa ParE domain of
S. pneumoniae
revealed that the most frequent mutations affected conserved residues, among them His43 and His103, which are involved in the hydrogen bond network supporting ATP hydrolysis, and Met31, at the dimeric interface. All mutants showed a particular phenotype of resistance to fluoroquinolones and an increase in susceptibility to novobiocin. All mutations in ParE resulted in resistance only when associated with a mutation in the QRDR of the GyrA subunit. Our models of the closed and open conformations of the active site indicate that quinolones preferentially target topoisomerase IV of
S. pneumoniae
in its ATP-bound closed conformation.
Identification of Three New Genes Involved in Morphogenesis and Antibiotic Production inStreptomyces coelicolor
Authors: Sprusansky Ondrej , Zhou Liqin , Jordan Sarah , White Jared , Westpheling Janet 
Published: October 2003

ABSTRACTWe report the isolation and partial characterization of three new mutants ofStreptomyces coelicolorthat are defective in morphogenesis and antibiotic production. The genes identified by the mutations were located and cloned by using a combination of Tn5in vitro mutagenesis, cotransformation, and genetic complementation. Mutant SE69 produces lower amounts of antibiotics than the wild type produces, produces spores only after prolonged incubation on rich media, and identifies a gene whose predicted protein product is similar to the GntR family of transcriptional regulators; also, production of aerial mycelia on both rich and poor media is significantly delayed in this mutant. Mutant SE293 is defective in morphogenesis, overproduces antibiotics on rich media, fails to grow on minimal media, and identifies a gene whose predicted protein product is similar to the TetR family of transcriptional regulators. Preliminary evidence suggests that the SE293 gene product may control a molybdopterin binding protein located immediately adjacent to it. Mutant SJ175 sporulates sooner and more abundantly than the wild type and overproduces antibiotics on rich media, and it identifies a gene whose predicted protein product contains regions of predominantly hydrophobic residues similar to those of integral membrane proteins.
Interfering with Different Steps of Protein SynthesisExplored by Transcriptional Profiling of
Escherichia coli
K-12
Authors: Sabina Jeffrey , Dover Nir , Templeton Lori J. , Smulski Dana R. , Söll Dieter , LaRossa Robert A. 
Published: October 2003

ABSTRACT

Escherichia
coli
responses to four inhibitors that interfere with translation
were monitored at the transcriptional level. A DNA microarray method
provided a comprehensive view of changes in mRNA levels after exposure
to these agents. Real-time reverse transcriptase PCRanalysis served to verify observations made with microarrays, and a
chromosomal
grpE
::
lux
operon
fusion was employed to specifically monitor the heat shock response.
4-Azaleucine, a competitive inhibitor of leucyl-tRNA synthetase,
surprisingly triggered the heat shock response. Administration of
mupirocin, an inhibitor of isoleucyl-tRNA synthetase activity, resulted
in changes reminiscent of the stringent response. Treatment with
kasugamycin and puromycin (targeting ribosomal subunit association as
well as its peptidyl-transferase activity) caused accumulation of mRNAs
from ribosomal protein operons. Abundant biosynthetic transcripts were
often significantly diminished after treatment with any of these
agents. Exposure of a
relA
strain to mupirocin resulted in
accumulation of ribosomal protein operon transcripts. However, the
relA
strain's response to the other inhibitors was quite
similar to that of the wild-type
strain.
A Second and Unusual
pucBA
Operon of
Rhodobacter sphaeroides
2.4.1: Genetics and Function of the Encoded Polypeptides
Authors: Zeng Xiaohua , Choudhary Madhu , Kaplan Samuel 
Published: October 2003

ABSTRACT

A new operon (designated the
puc2BA
operon) displaying a high degree of similarity to the original
pucBA
genes of
Rhodobacter sphaeroides
2.4.1 (designated
puc1
) was identified and studied genetically and biochemically. The
puc2B
-encoded polypeptide is predicted to exhibit 94% identity with the original β-apoprotein. The
puc2A
-encoded polypeptide is predicted to be much larger (263 amino acids) than the 54-amino-acid
puc1A
-encoded polypeptide. In the first 48 amino acids of the
puc2A
-encoded polypeptide there is 58% amino acid sequence identity to the original
puc1A
-encoded polypeptide. We found that
puc2BA
is expressed, and DNA sequence data suggested that
puc2BA
is regulated by the PpsR/AppA repressor-antirepressor and FnrL. Employing genetic and biochemical approaches, we obtained evidence that the
puc2B
-encoded polypeptide is able to enter into LH2 complex formation, but neither the full-length
puc2A
-encoded polypeptide nor its N-terminal 48-amino-acid derivative is able to enter into LH2 complex formation. Thus, the sole source of α-polypeptides for the LH2 complex is
puc1A
. The role of the
puc1C
-encoded polypeptide was also determined. We found that the presence of this polypeptide is essential for normal levels of transcription and translation of the
puc1
operon but not for transcription and translation of the
puc2
operon. Thus, the
puc1C
gene product appears to have both transcriptional and posttranscriptional roles in LH2 formation. Finally, the absence of any LH2 complex when
puc1B
was deleted in frame was surprising since we know that in the presence of functional
puc2BA
, approximately 30% of the LH2 complexes normally observed contain a
puc2B
-encoded β-polypeptide.
Changes inEscherichia colirRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis
Authors: Schneider David A. , Gourse Richard L. 
Published: October 2003

ABSTRACTrRNA synthesis is the rate-limiting step in ribosome synthesis inEscherichia coli. Its regulation has been described in terms of a negative-feedback control loop in which rRNA promoter activity responds to the amount of translation. The feedback nature of this control system was demonstrated previously by artificially changing ribosome synthesis rates and observing responses of rRNA promoters. However, it has not been demonstrated previously that the initiating nucleoside triphosphate (iNTP) and guanosine 5′-diphosphate 3′-diphosphate (ppGpp), the molecular effectors responsible for controlling rRNA promoters in response to changes in the nutritional environment, are responsible for altering rRNA promoter activities under these feedback conditions. Here, we show that most feedback situations result in changes in the concentrations of both the iNTP and ppGpp and that the directions of these changes are consistent with a role for these two small-molecule regulators in feedback control of rRNA synthesis. In contrast, we observed no change in the level of DNA supercoiling under the feedback conditions examined.
Reduced Water Availability Influences the Dynamics, Development, and Ultrastructural Properties of
Pseudomonas putida
Biofilms
Authors: Chang Woo-Suk , Halverson Larry J. 
Published: October 2003

ABSTRACT

Pseudomonas putida
strain mt-2 unsaturated biofilm formation proceeds through three distinct developmental phases, culminating in the formation of a microcolony. The form and severity of reduced water availability alter cell morphology, which influences microcolony size and ultrastructure. The dehydration (matric stress) treatments resulted in biofilms comprised of smaller cells, but they were taller and more porous and had a thicker extracellular polysaccharide layer at the air interface. In the solute stress treatments, cell filamentation occurred more frequently in the presence of high concentrations of ionic (but not nonionic) solutes, and these filamented cells drastically altered the biofilm architecture.
Characterization of
divIVA
and Other Genes Located in the Chromosomal Region Downstream of the
dcw
Cluster in
Streptococcus pneumoniae
Authors: Fadda Daniela , Pischedda Carla , Caldara Fabrizio , Whalen Michael B. , Anderluzzi Daniela , Domenici Enrico , Massidda Orietta 
Published: October 2003

ABSTRACT

We analyzed the chromosome region of
Streptococcus pneumoniae
located downstream of the division and cell wall (
dcw
) cluster that contains the homolog of the
Bacillus subtilis
cell division gene
divIVA
and some genes of unknown function. Inactivation of
divIVA
in
S. pneumoniae
resulted in severe growth inhibition and defects in cell shape, nucleoid segregation, and cell division. Inactivation of the
ylm
genes resulted in some morphological and/or division abnormalities, depending on the inactivated gene. Transcriptional analysis revealed a relationship between these genes and the
ftsA
and
ftsZ
cell division genes, also indicating that the connection between the
dcw
cluster and the
divIVA
region is more extensive than just chromosomal position and gene organization.