bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geobacter sulfurreducensHas Two AutoregulatedlexAGenes Whose Products Do Not Bind therecAPromoter: Differing Responses oflexAandrecAto DNA Damage
Authors: Jara Mónica , Núñuz Cinthia , Campoy Susana , Fernández de Henestrosa Antonio R. , Lovley Derek R. , Barbé Jordi 
Published: April 2003

ABSTRACTTheEscherichia coliLexA protein was used as a query sequence in TBLASTN searches to identify thelexAgene of the δ-proteobacteriumGeobacter sulfurreducensfrom its genome sequence. The results of the search indicated thatG. sulfurreducenshas two independentlexAgenes designatedlexA1andlexA2. A copy of adinBgene homologue, which inE. coliencodes DNA polymerase IV, is present downstream of eachlexAgene. Reverse transcription-PCR analyses demonstrated that, in both cases,lexAanddinBconstitute a single transcriptional unit. Electrophoretic mobility shift assays with purified LexA1 and LexA2 proteins have shown that both proteins bind the imperfect palindrome GGTTN2CN4GN3ACC found in the promoter region of bothlexA1andlexA2. This sequence is also present upstream of theGeobacter metallireducens lexAgene, indicating that it is the LexA box of this bacterial genus. This palindrome is not found upstream of either theG. sulfurreducensor theG. metallireducens recAgenes. Furthermore, DNA damage induces expression of thelexA-dinBtranscriptional unit but not that of therecAgene. However, the basal level ofrecAgene expression is dramatically higher than that of thelexAgene. Likewise, the promoters of theG. sulfurreducens recN,ruvAB,ssb,umuDC,uvrA, anduvrBgenes do not contain the LexA box and are not likely to bind to the LexA1 or LexA2 proteins.G. sulfurreducensis the first bacterial species harboring alexAgene for which a constitutive expression of itsrecAgene has been described.
Membrane Topology of PssT, the Transmembrane Protein Component of the Type I Exopolysaccharide Transport System in
Rhizobium leguminosarum
bv. trifolii Strain TA1
Authors: Mazur Andrzej , Król Jarosław E. , Marczak Małgorzata , Skorupska Anna 
Published: April 2003

ABSTRACT

The
pssT
gene was identified as the fourth gene located upstream of the
pssNOP
gene cluster possibly involved in the biosynthesis, polymerization, and transport of exopolysaccharide (EPS) in
Rhizobium leguminosarum
bv. trifolii strain TA1. The hydropathy profile and homology searches indicated that PssT belongs to the polysaccharide-specific transport family of proteins, a component of the type I system of the polysaccharide transport. The predicted membrane topology of the PssT protein was examined with a series of PssT-PhoA fusion proteins and a complementary set of PssT-LacZ fusions. The results generally support a predicted topological model for PssT consisting of 12 transmembrane segments, with amino and carboxyl termini located in the cytoplasm. A mutant lacking the C-terminal part of PssT produced increased amounts of total EPS with an altered distribution of high- and low-molecular-weight forms in comparison to the wild-type RtTA1 strain. The PssT mutant produced an increased number of nitrogen fixing nodules on clover.
Regulation of the Alternative Sigma Factor σ
E
during Initiation, Adaptation, and Shutoff of the Extracytoplasmic Heat Shock Response in
Escherichia coli
Authors: Ades Sarah E. , Grigorova Irina L. , Gross Carol A. 
Published: April 2003

ABSTRACT

The alternative sigma factor σ
E
is activated in response to stress in the extracytoplasmic compartment of
Escherichia coli
. Here we show that σ
E
activity increases upon initiation of the stress response by a shift to an elevated temperature (43°C) and remains at that level for the duration of the stress. When the stress is removed by a temperature downshift, σ
E
activity is strongly repressed and then slowly returns to levels seen in unstressed cells. We provide evidence that information about the state of the cell envelope is communicated to σ
E
primarily through the regulated proteolysis of the inner membrane anti-sigma factor RseA, as the degradation rate of RseA is correlated with the changes in σ
E
activity throughout the stress response. However, the relationship between σ
E
activity and the rate of degradation of RseA is complex, indicating that other factors may cooperate with RseA and serve to fine-tune the response.
Transcription of
Clostridium cellulovorans
Cellulosomal Cellulase and Hemicellulase Genes
Authors: Han Sung Ok , Yukawa Hideaki , Inui Masayuki , Doi Roy H. 
Published: April 2003

ABSTRACT

Transcription of the cellulosomal cellulase/hemicellulase genes of
Clostridium cellulovorans
has been investigated by Northern blot, reverse transcriptase PCR (RT-PCR), primer extension, and S1 nuclease analysis. Northern hybridizations revealed that the cellulosomal
cbpA
gene cluster is transcribed as polycistronic mRNAs of 8 and 12 kb. The 8-kb mRNA coded for
cbpA
and
exgS
, and the 12-kb mRNA coded for
cbpA
,
exgS
,
engH
, and
engK
. The sizes of the mRNAs were about 3 kb for
engE
, 1.8 kb for
manA
, 2.7 kb for
xynA
, and 4 kb for
pelA
, indicating monocistronic transcription of these genes. Primer extension and S1 nuclease analysis of
C. cellulovorans
RNA showed that the transcriptional start sites of
cbpA
,
engE
,
manA
, and
hbpA
were located 233, 97, 64, and 61 bp upstream from the first nucleotide of each of the respective translation initiation codons. Alignment of the
cbpA
,
engE
,
manA
, and
hbpA
promoter regions provided evidence for highly conserved sequences that exhibited strong similarity to the σ
A
consensus promoter sequences of gram-positive bacteria.
Porphyrin-Mediated Cell Surface Heme Capture from Hemoglobin byPorphyromonas gingivalis
Authors: Paramaesvaran Mayuri , Nguyen Ky-Anh , Caldon Elizabeth , McDonald James A. , Najdi Sherean , Gonzaga Graciel , Langley David B. , DeCarlo Arthur , Crossley Maxwell J. , Hunter Neil , Collyer Charles A. 
Published: April 2003

ABSTRACTThe porphyrin requirements for growth recovery ofPorphyromonas gingivalisin heme-depleted cultures are investigated. In addition to physiologically relevant sources of heme, growth recovery is stimulated by a number of noniron porphyrins. These data demonstrate that, as forHaemophilus influenzae, reliance on captured iron and on exogenous porphyrin is manifest as an absolute growth requirement for heme. A number of outer membrane proteins including some gingipains contain the hemoglobin receptor (HA2) domain. In cell surface extracts, polypeptides derived from HA2-containing proteins predominated in hemoglobin binding. The in vitro porphyrin-binding properties of a recombinant HA2 domain were investigated and found to be iron independent. Porphyrins that differ from protoporphyrin IX in only the vinyl aspect of the tetrapyrrole ring show comparable effects in competing with hemoglobin for HA2 and facilitate growth recovery. For some porphyrins which differ from protoporphyrin IX at both propionic acid side chains, the modification is detrimental in both these assays. Correlations of porphyrin competition and growth recovery imply that the HA2 domain acts as a high-affinity hemophore at the cell surface to capture porphyrin from hemoglobin. While some proteins involved with heme capture bind directly to the iron center, the HA2 domain ofP. gingivalisrecognizes heme by a mechanism that is solely porphyrin mediated.
Homologue of Macrophage-Activating Lipoprotein in
Mycoplasma
gallisepticum
Is Not Essential for Growth and Pathogenicity in Tracheal Organ Cultures
Authors: Markham Philip F. , Kanci Anna , Czifra György , Sundquist Bo , Hains Peter , Browning Glenn F. 
Published: April 2003

ABSTRACT

While the genomes of a number of
Mycoplasma
species have been fully determined, there has been limited characterization of which genes are essential. The surface protein (p47) identified by monoclonal antibody B3 is the basis for an enzyme-linked immunosorbent assay for serological detection of
Mycoplasma
gallisepticum
infection and appears to be constitutively expressed. Its gene was cloned, and the DNA sequence was determined. Subsequent analysis of the p47 amino acid sequence and searches of DNA databases found homologous gene sequences in the genomes of
M
.
pneumoniae
and
M
.
genitalium
and identity with a gene family in
Ureaplasma
urealyticum
and genes in
M
.
agalactiae
and
M
.
fermentans
. The proteins encoded by these genes were found to belong to a family of basic membrane proteins (BMP) that are found in a wide range of bacteria, including a number of pathogens. Several of the BMP family members, including p47, contain selective lipoprotein-associated motifs that are found in macrophage-activating lipoprotein 404 of
M
.
fermentans
and lipoprotein P48 of
M
.
agalactiae
. The
p47
gene was predicted to encode a 59-kDa peptide, but affinity-purified p47 had a molecular mass of approximately 47 kDa, as determined by polyacrylamide gel analysis. Analysis of native and recombinant p47 by mass peptide fingerprinting revealed the absence of the carboxyl end of the protein encoded by the
p47
gene in native p47, which would account for the difference seen in the predicted and measured molecular weights and indicated posttranslational cleavage of the lipoprotein at its carboxyl end. A DNA construct containing the
p47
gene interrupted by the gene encoding tetracycline resistance was used to transform
M
.
gallisepticum
cells. A tetracycline-resistant mycoplasma clone, P2, contained the construct inserted within the genomic
p47
gene, with crossovers occurring between 73 bp upstream and 304 bp downstream of the inserted tetracycline resistance gene. The absence of p47 protein in clone P2 was determined by the lack of reactivity with rabbit anti-p47 sera or monoclonal antibody B3 in Western blots of whole-cell proteins. There was no difference between the p47
−
mutant and wild-type
M
.
gallisepticum
in pathogenicity in chicken tracheal organ cultures. Thus,
p47
, although homologous to genes that occur in many prokaryotes, is not essential for growth in vitro or for attachment and the initial stages of pathogenesis in chickens.
Function and Regulation of the Formate Dehydrogenase Genes of the Methanogenic ArchaeonMethanococcus maripaludis
Authors: Wood Gwendolyn E. , Haydock Andrew K. , Leigh John A. 
Published: April 2003

ABSTRACTMethanococcus maripaludisis a mesophilic species ofArchaeacapable of producing methane from two substrates: hydrogen plus carbon dioxide and formate. To study the latter, we identified the formate dehydrogenase genes ofM. maripaludisand found that the genome contains two gene clusters important for formate utilization. Phylogenetic analysis suggested that the two formate dehydrogenase gene sets arose from duplication events within the methanococcal lineage. The first gene cluster encodes homologs of formate dehydrogenase α (FdhA) and β (FdhB) subunits and a putative formate transporter (FdhC) as well as a carbonic anhydrase analog. The second gene cluster encodes only FdhA and FdhB homologs. Mutants lacking eitherfdhAgene exhibited a partial growth defect on formate, whereas a double mutant was completely unable to grow on formate as a sole methanogenic substrate. Investigation offdhgene expression revealed that transcription of both gene clusters is controlled by the presence of H2and not by the presence of formate.
Evolutionary Relationships among Strains of
Mycobacterium tuberculosis
with Few Copies of IS
6110
Authors: Dale Jeremy W. , Al-Ghusein Hasan , Al-Hashmi Salim , Butcher Philip , Dickens Anne L. , Drobniewski Francis , Forbes Ken J. , Gillespie Stephen H. , Lamprecht Dianie , McHugh Timothy D. , Pitman Richard , Rastogi Nalin , Smith Andrew T. , Sola Christophe , Yesilkaya Hasan 
Published: April 2003

ABSTRACT

Molecular typing of
Mycobacterium tuberculosis
by using IS
6110
shows low discrimination when there are fewer than five copies of the insertion sequence. Using a collection of such isolates from a study of the epidemiology of tuberculosis in London, we have shown a substantial degree of congruence between IS
6110
patterns and both spoligotype and PGRS type. This indicates that the IS
6110
types mainly represent distinct families of strains rather than arising through the convergent insertion of IS
6110
into favored positions. This is supported by identification of the genomic sites of the insertion of IS
6110
in these strains. The combined data enable identification of the putative evolutionary relationships of these strains, comprising three lineages broadly associated with patients born in South Asia (India and Pakistan), Africa, and Europe, respectively. These lineages appear to be quite distinct from
M. tuberculosis
isolates with multiple copies of IS
6110
.
Repression of
Escherichia coli
PhoP-PhoQ Signaling by Acetate Reveals a Regulatory Role for Acetyl Coenzyme A
Authors: Lesley Joseph A. , Waldburger Carey D. 
Published: April 2003

ABSTRACT

The PhoP-PhoQ two-component system regulates the transcription of numerous genes in response to changes in extracellular divalent cation concentration and pH. Here we demonstrate that the
Escherichia coli
PhoP-PhoQ two-component system also responds to acetate. Signaling by the
E
.
coli
PhoP-PhoQ system was repressed during growth in acetate (≥25 mM) in a PhoQ-dependent manner. The periplasmic sensor domain of PhoQ was not required for acetate to repress signaling. Acetate-mediated repression of the PhoP-PhoQ system was not related to changes in the intracellular concentration of acetate metabolites such as acetyl-phosphate or acetyladenylate. Genetic analysis of acetate metabolism pathways suggested that a perturbation of acetyl coenzyme A turnover was the cause of decreased PhoP-PhoQ signaling during growth in acetate. Consistent with this hypothesis, intracellular acetyl coenzyme A levels rose during growth in the presence of exogenous acetate. Acetyl coenzyme A inhibited the autokinase activity of PhoQ in vitro, suggesting that the in vivo repressing effect may be due to a direct inhibition mechanism.
Genomic Diversity and Relatedness of Bifidobacteria Isolated from a Porcine Cecum
Authors: Simpson P. J. , Stanton C. , Fitzgerald G. F. , Ross R. P. 
Published: April 2003

ABSTRACTThis study initially involved the isolation of a number of bifidobacteria from either the lumen or the epithelium of a porcine cecum. A total of 160 isolates were selected at random on MRS plates containing cysteine hydrochloride (0.5 g/liter) and mupirocin (50 mg/liter). All were identified as bifidobacteria based on fructose-6-phosphate phosphoketolase activity. Following genomic digestion with the restriction enzymeXbaI and pulsed-field gel electrophoresis (PFGE), the isolates produced 15 distinct macro-restriction patterns. Several of the PFGE patterns differed by only 1, 2, or 3 DNA fragments and were grouped as related patterns into seven PFGE types, termed A through G. The related patterns appeared to show genomic plasticity within the isolates arising from chromosomal mutations or possibly horizontal transfer of plasmids. The relative frequency of each PFGE type was maintained within each cecal sample, with PFGE type E representing approximately 50% of the isolates. Randomly amplified polymorphic DNA PCR, cell morphology, whole-cell protein profiling, 16S ribosomal DNA sequencing, and DNA-DNA hybridization were used to determine if the seven apparently unrelated PFGE types represented genetically distinct isolates. Four groups were identified: PFGE types A, C/D/G, B/E, and F, and these appeared to representBifidobacterium minimum, Bifidobacterium pseudolongumsubsp. pseudolongum,andBifidobacterium pseudolongumsubsp.globosumand two new species, respectively. The data demonstrate the presence of considerable genomic diversity within a relatively simple bifidobacteria population, consisting of 15 distinct strains representing four groups, which was maintained throughout the porcine cecal contents and epithelial layer.
Signal Transduction Protein P
II
Is Required for NtcA-Regulated Gene Expression during Nitrogen Deprivation in the Cyanobacterium
Synechococcus elongatus
Strain PCC 7942
Authors: Fadi Aldehni M. , Sauer Jörg , Spielhaupter Christian , Schmid Roland , Forchhammer Karl 
Published: April 2003

ABSTRACT

The transcription factor of the cyclic AMP receptor protein/FNR family, NtcA, and the P
II
signaling protein play central roles in global nitrogen control in cyanobacteria. A dependence on P
II
for NtcA-regulated transcription, however, has not been observed. In the present investigation, we examined alterations in gene expression following nitrogen deprivation in
Synechococcus elongatus
strain PCC 7942 and specifically the roles of NtcA and P
II
. Global changes in de novo protein synthesis following combined-nitrogen deprivation were visualized by in vivo [
35
S]methionine labeling and two-dimensional polyacrylamide gel electrophoresis analysis. Nearly all proteins whose synthesis responded specifically to combined-nitrogen deprivation in wild-type cells of
S. elongatus
failed to respond in P
II
- and NtcA-deficient mutants. One of the proteins whose synthesis was down-regulated in a P
II
- and NtcA-dependent manner was RbcS, the small subunit of RubisCO. Quantification of its mRNA revealed that the abundance of the
rbcLS
transcript following combined-nitrogen deprivation rapidly declined in wild-type cells but not in P
II
and NtcA mutant cells. To investigate further the relationship between P
II
and NtcA, fusions of the promotorless
luxAB
reporter genes to the NtcA-regulated
glnB
gene were constructed and these constructs were used to transform wild-type cells and P
II
−
and NtcA
−
mutants. Determination of bioluminescence under different growth conditions showed that NtcA represses gene expression in the presence of ammonium in a P
II
-independent manner. By contrast, NtcA-dependent activation of
glnB
expression following combined-nitrogen deprivation was impaired in the absence of P
II
. Together, these results suggest that under conditions of combined-nitrogen deprivation, the regulation of NtcA-dependent gene expression requires the P
II
signal transduction protein.
Pseudomonas syringae
Exchangeable Effector Loci: Sequence Diversity in Representative Pathovars and Virulence Function in
P. syringae
pv. syringae B728a
Authors: Deng Wen-Ling , Rehm Amos H. , Charkowski Amy O. , Rojas Clemencia M. , Collmer Alan 
Published: April 2003

ABSTRACT

Pseudomonas syringae
is a plant pathogen whose pathogenicity and host specificity are thought to be determined by Hop/Avr effector proteins injected into plant cells by a type III secretion system.
P. syringae
pv. syringae B728a, which causes brown spot of bean, is a particularly well-studied strain. The type III secretion system in
P. syringae
is encoded by
hrp
(hypersensitive response and pathogenicity) and
hrc
(
hrp
conserved) genes, which are clustered in a pathogenicity island with a tripartite structure such that the
hrp
/
hrc
genes are flanked by a conserved effector locus and an exchangeable effector locus (EEL). The EELs of
P. syringae
pv. syringae B728a,
P. syringae
strain 61, and
P. syringae
pv. tomato DC3000 differ in size and effector gene composition; the EEL of
P. syringae
pv. syringae B728a is the largest and most complex. The three putative effector proteins encoded by the
P. syringae
pv. syringae B728a EEL—HopPsyC, HopPsyE, and HopPsyV—were demonstrated to be secreted in an Hrp-dependent manner in culture. Heterologous expression of
hopPsyC
,
hopPsyE
, and
hopPsyV
in
P. syringae
pv. tabaci induced the hypersensitive response in tobacco leaves, demonstrating avirulence activity in a nonhost plant. Deletion of the
P. syringae
pv. syringae B728a EEL strongly reduced virulence in host bean leaves. EELs from nine additional strains representing nine
P. syringae
pathovars were isolated and sequenced. Homologs of
avrPphE
(e.g.,
hopPsyE
) and
hopPsyA
were particularly common. Comparative analyses of these effector genes and
hrpK
(which flanks the EEL) suggest that the EEL effector genes were acquired by horizontal transfer after the acquisition of the
hrp
/
hrc
gene cluster but before the divergence of modern pathovars and that some EELs underwent transpositions yielding effector exchanges or point mutations producing effector pseudogenes after their acquisition.
Peptide-Peptide Interactions between Human Transferrin and Transferrin-Binding Protein B from
Moraxella
catarrhalis
Authors: Sims Kurtis L. , Schryvers Anthony B. 
Published: April 2003

ABSTRACT

Transferrin-binding protein B (TbpB) is one component of a bipartite receptor in several gram-negative bacterial species that binds host transferrin and mediates the uptake of iron for growth. Transferrin and TbpB are both bilobed proteins, and the interaction between these proteins seems to involve similar lobe-lobe interactions. Synthetic overlapping peptide libraries representing the N lobe of TbpB from
Moraxella
catarrhalis
were prepared and probed with labeled human transferrin. Transferrin-binding peptides were localized to six different regions of the TbpB N lobe, and reciprocal experiments identified six different regions of the C lobe of transferrin that bound TbpB. Truncations of the N lobe of TbpB that sequentially removed each transferrin-binding determinant were used to probe an overlapping peptide library of the C lobe of human transferrin. The removal of each TbpB N-lobe transferrin-binding determinant resulted in a loss of reactivity with peptides from the synthetic peptide library representing the C lobe of transferrin. Thus, individual peptide-peptide interactions between ligand and receptor were identified. A structural model of human transferrin was used to map surface regions capable of binding to TbpB.
Three-Dimensional Structure of the
Neisseria meningitidis
Secretin PilQ Determined from Negative-Stain Transmission Electron Microscopy
Authors: Collins Richard F. , Ford Robert C. , Kitmitto Ashraf , Olsen Ranveig O. , Tønjum Tone , Derrick Jeremy P. 
Published: April 2003

ABSTRACT

The PilQ secretin from the pathogenic bacterium
Neisseria meningitidis
is an integral outer membrane protein complex which plays a crucial role in the biogenesis of type IV pili. We present here the first three-dimensional structure of this type of secretin at 2.5-nm resolution, obtained by single-particle averaging methods applied to the purified protein complex visualized in a negative stain. In projection, the PilQ complex is circular, with a donut-like appearance. When viewed from the side it has a rounded, conical profile. The complex was demonstrated to have 12-fold rotational symmetry, and this property was used to improve the quality of the density map by symmetry averaging. The dominant feature of the structure is a cavity, 10 nm deep, within the center of the molecule. The cavity is funnel-shaped in cross section, measures 6.5 nm in diameter at the top of the complex, and tapers to a closed point, effectively blocking formation of a continuous pore through the PilQ complex. These results suggest that the complex would have to undergo a conformational change in order to accommodate an assembled pilus fiber of diameter 6.5 nm running through the outer membrane.