bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Conserved Histidine in Cytochrome
c
Maturation Permease CcmB of
Shewanella putrefaciens
Is Required for Anaerobic Growth below a Threshold Standard Redox Potential
Authors: Dale Jason R. , Wade Roy , DiChristina Thomas J. 
Published: December 2006

ABSTRACT

Shewanella putrefaciens
strain 200 respires a wide range of compounds as terminal electron acceptor. The respiratory versatility of
Shewanella
is attributed in part to a set of
c
-type cytochromes with widely varying midpoint redox potentials (E′
0
). A point mutant of
S. putrefaciens
, originally designated Urr14 and here renamed CCMB1, was found to grow at wild-type rates on electron acceptors with high E′
0
[O
2
, NO
3
−
, Fe(III) citrate, MnO
2
, and Mn(III) pyrophosphate] yet was severely impaired for growth on electron acceptors with low E′
0
[NO
2
−
, U(VI), dimethyl sulfoxide, TMAO (trimethylamine
N
-oxide), fumarate, γ-FeOOH, SO
3
2−
, and S
2
O
3
2−
]. Genetic complementation and nucleotide sequence analyses indicated that the CCMB1 respiratory mutant phenotype was due to mutation of a conserved histidine residue (H108Y) in a protein that displayed high homology to
Escherichia coli
CcmB, the permease subunit of an ABC transporter involved in cytochrome
c
maturation. Although CCMB1 retained the ability to grow on electron acceptors with high E′
0
, the cytochrome content of CCMB1 was <10% of that of the wild-type strain. Periplasmic extracts of CCMB1 contained slightly greater concentrations of the thiol functional group (-SH) than did the wild-type strain, an indication that the E
h
of the CCMB1 periplasm was abnormally low. A
ccmB
deletion mutant was unable to respire anaerobically on any electron acceptor, yet retained aerobic respiratory capability. These results suggest that the mutation of a conserved histidine residue (H108) in CCMB1 alters the redox homeostasis of the periplasm during anaerobic growth on electron acceptors with low (but not high) E′
0
. This is the first report of the effects of Ccm deficiencies on bacterial respiration of electron acceptors whose E′
0
nearly span the entire redox continuum.
Regulation of
Aggregatibacter
(
Actinobacillus
)
actinomycetemcomitans
Leukotoxin Secretion by Iron
Authors: Balashova Nataliya V. , Diaz Roger , Balashov Sergey V. , Crosby Juan A. , Kachlany Scott C. 
Published: December 2006

ABSTRACT

The gram-negative oral and systemic pathogen
Aggregatibacter
(
Actinobacillus
)
actinomycetemcomitans
produces a leukotoxin (LtxA) that is a member of the RTX (repeats in toxin) family of secreted bacterial toxins. We have recently shown that LtxA has the ability to lyse erythrocytes, which results in a beta-hemolytic phenotype on Columbia blood agar. To determine if LtxA is regulated by iron, we examined beta-hemolysis under iron-rich and iron-limiting conditions. Beta-hemolysis was suppressed in the presence of FeCl
3
. In contrast, strong beta-hemolysis occurred in the presence of the iron chelator deferoxamine. We found that secretion of LtxA was completely inhibited by free iron, but expression of
ltxA
was not regulated by iron. Free chromium, cobalt, and magnesium did not affect LtxA secretion. Other LtxA-associated genes were not regulated by iron. Thus, iron appears to play an important role in the regulation of LtxA secretion in
A. actinomycetemcomitans
in a manner independent of gene regulation.
NrrA Directly Regulates Expression of
hetR
during Heterocyst Differentiation in the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Ehira Shigeki , Ohmori Masayuki 
Published: December 2006

ABSTRACT

Heterocyst differentiation in the cyanobacterium
Anabaena
sp. strain PCC 7120 requires NtcA, the global nitrogen regulator in cyanobacteria, and HetR, the master regulator of heterocyst differentiation. Expression of
hetR
is upregulated by nitrogen deprivation, and its upregulation depends on NtcA. However, it has not yet been revealed how NtcA regulates the expression of
hetR
. In the experiments presented here, it was confirmed that NrrA (All4312), a nitrogen-responsive response regulator, was required for the upregulation of
hetR
. The use of the nitrogen-responsive transcription initiation sites (TISs) for the
hetR
gene depended upon NrrA. NrrA bound specifically to the region upstream of TISs located at positions −728 and −696 in vitro. Overexpression of
nrrA
resulted in enhanced
hetR
expression and heterocyst formation. A molecular regulatory cascade is proposed whereby NtcA upregulates the expression of
nrrA
upon limitation of combined nitrogen in the medium and then NrrA upregulates the expression of
hetR
, leading to heterocyst differentiation.
Mutation in a “
tesB
-Like” Hydroxyacyl-Coenzyme A-Specific Thioesterase Gene Causes Hyperproduction of Extracellular Polyhydroxyalkanoates by
Alcanivorax borkumensis
SK2
Authors: Sabirova Julia S. , Ferrer Manuel , Lünsdorf Heinrich , Wray Victor , Kalscheuer Rainer , Steinbüchel Alexander , Timmis Kenneth N. , Golyshin Peter N. 
Published: December 2006

ABSTRACT

A novel mutant of the marine oil-degrading bacterium
Alcanivorax borkumensis
SK2, containing a mini-Tn
5
transposon disrupting a “
tesB
-like” acyl-coenzyme A (CoA) thioesterase gene, was found to hyperproduce polyhydroxyalkanoates (PHA), resulting in the extracellular deposition of this biotechnologically important polymer when grown on alkanes. The
tesB
-like gene encodes a distinct novel enzyme activity, which acts exclusively on hydroxylated acyl-CoAs and thus represents a hydroxyacyl-CoA-specific thioesterase. Inactivation of this enzyme results in the rechanneling of CoA-activated hydroxylated fatty acids, the cellular intermediates of alkane degradation, towards PHA production. These findings may open up new avenues for the development of simplified biotechnological processes for the production of PHA as a raw material for the production of bioplastics.
Transcriptomic Analysis Reveals a Bifurcated Terephthalate Degradation Pathway in
Rhodococcus
sp. Strain RHA1
Authors: Hara Hirofumi , Eltis Lindsay D. , Davies Julian E. , Mohn William W. 
Published: December 2006

ABSTRACT

Phthalate isomers and their esters are important pollutants whose biodegradation is not well understood.
Rhodococcus
sp. strain RHA1 is notable for its ability to degrade a wide range of aromatic compounds. RHA1 was previously shown to degrade phthalate (PTH) and to have genes putatively encoding terephthalate (TPA) degradation. Transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on PTH and that 521 were up-regulated during growth on TPA. Distinct ring cleavage dioxygenase systems were differentially expressed during growth on PTH and TPA. Genes encoding the protocatechuate (PCA) pathway were induced on both substrates, while genes encoding the catechol branch of the PCA pathway were additionally induced only on TPA. Accordingly, protocatechuate-3,4-dioxygenase activity was induced in cells grown on both substrates, while catechol-1,2-dioxygenase activity was induced only in cells grown on TPA. Knockout analysis indicated that
pcaL
, encoding 3-oxoadipate enol-lactone hydrolase and 4-carboxymuconolactone decarboxylase, was required for growth on both substrates but that
pcaB
, encoding β-carboxy-
cis
,
cis
-muconate lactonizing enzyme, was required for growth on PTH only. These results indicate that PTH is degraded solely via the PCA pathway, whereas TPA is degraded via a bifurcated pathway that additionally includes the catechol branch of the PCA pathway.
nalD
Encodes a Second Repressor of the
mexAB-oprM
Multidrug Efflux Operon of
Pseudomonas aeruginosa
Authors: Morita Yuji , Cao Lily , Gould Virginia C. , Avison Matthew B. , Poole Keith 
Published: December 2006

ABSTRACT

The
Pseudomonas aeruginosa nalD
gene encodes a TetR family repressor with homology to the SmeT and TtgR repressors of the
smeDEF
and
ttgABC
multidrug efflux systems of
Stenotrophomonas maltophilia
and
Pseudomonas putida
, respectively. A sequence upstream of
mexAB-oprM
and overlapping a second promoter for this efflux system was very similar to the SmeT and TtgR operator sequences, and NalD binding to this region was, in fact, demonstrated. Moreover, increased expression from this promoter was seen in a
nalD
mutant, consistent with NalD directly controlling
mexAB-oprM
expression from a second promoter.
Analysis of Proline Reduction in the Nosocomial Pathogen
Clostridium difficile
Authors: Jackson Sarah , Calos Mary , Myers Andrew , Self William T. 
Published: December 2006

ABSTRACT

Clostridium difficile
, a proteolytic strict anaerobe, has emerged as a clinically significant nosocomial pathogen in recent years. Pathogenesis is due to the production of lethal toxins, A and B, members of the large clostridial cytotoxin family. Although it has been established that alterations in the amino acid content of the growth medium affect toxin production, the molecular mechanism for this observed effect is not yet known. Since there is a paucity of information on the amino acid fermentation pathways used by this pathogen, we investigated whether Stickland reactions might be at the heart of its bioenergetic pathways. Growth of
C. difficile
on Stickland pairs yielded large increases in cell density in a limiting basal medium, demonstrating that these reactions are tied to ATP production. Selenium supplementation was required for this increase in cell yield. Analysis of genome sequence data reveals genes encoding the protein components of two key selenoenzyme reductases, glycine reductase and
d
-proline reductase (PR). These selenoenzymes were expressed upon the addition of the corresponding Stickland acceptor (glycine, proline, or hydroxyproline). Purification of the selenoenzyme
d
-proline reductase revealed a mixed complex of PrdA and PrdB (SeCys-containing) proteins. PR utilized only
d
-proline but not
l
-hydroxyproline, even in the presence of an expressed and purified proline racemase. PR was found to be independent of divalent cations, and zinc was a potent inhibitor of PR. These results show that Stickland reactions are key to the growth of
C. difficile
and that the mechanism of PR may differ significantly from that of previously studied PR from nonpathogenic species.
RhlR Expression inPseudomonas aeruginosaIs Modulated by thePseudomonasQuinolone Signal via PhoB-Dependent and -Independent Pathways
Authors: Jensen Vanessa , Löns Dagmar , Zaoui Caroline , Bredenbruch Florian , Meissner Andree , Dieterich Guido , Münch Richard , Häussler Susanne 
Published: December 2006

ABSTRACTThe expression of virulence determinants inPseudomonas aeruginosais coordinately regulated in response to both the social environment—commonly referred to as quorum sensing—and to environmental cues. In this study we have dissected the various independent regulation levels for pyocyanin production, which is influenced by the homoserine lactone- andPseudomonasquinolone signal (PQS)-mediated quorum-sensing systems as well as by iron and phosphate availability. We demonstrate that the phosphate regulon is involved in the transcriptional activation ofrhlRand the augmentation of PQS and pyocyanin production under phosphate limitation. However, we also observed an enhancement ofrhlRtranscription under low-iron medium conditions and after the addition of PQS that was independent of the phosphate regulon. These results highlight the complexity of secondary metabolite production inP. aeruginosavia environmental cues and the quorum-sensing system.
Similarity and Differences in the
Lactobacillus acidophilus
Group Identified by Polyphasic Analysis and Comparative Genomics
Authors: Berger Bernard , Pridmore R. David , Barretto Caroline , Delmas-Julien Françoise , Schreiber Kerstin , Arigoni Fabrizio , Brüssow Harald 
Published: December 2006

ABSTRACT

A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the
Lactobacillus acidophilus
complex. On microarray analysis, 17 and 5% of the genes from
Lactobacillus johnsonii
strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of
L. johnsonii
. When projected on the NCC533 genome map, about 10 large clusters of variable genes were identified, and they were enriched around the terminus of replication. A quarter of the variable genes and two-thirds of the strain-specific genes were associated with mobile DNA. Signatures for horizontal gene transfer and modular evolution were found in prophages and in DNA from the exopolysaccharide biosynthesis cluster. On microarray hybridizations,
Lactobacillus gasseri
strains showed a shift to significantly lower fluorescence intensities than the
L. johnsonii
test strains, and only genes encoding very conserved cellular functions from
L. acidophilus
hybridized to the
L. johnsonii
array. In-silico comparative genomics showed extensive protein sequence similarity and genome synteny of
L. johnsonii
with
L. gasseri
,
L. acidophilus
, and
Lactobacillus delbrueckii
; moderate synteny with
Lactobacillus casei
; and scattered X-type sharing of protein sequence identity with the other sequenced lactobacilli. The observation of a stepwise decrease in similarity between the members of the
L. acidophilus
group suggests a strong element of vertical evolution in a natural phylogenetic group. Modern whole-genome-based techniques are thus a useful adjunct to the clarification of taxonomical relationships in problematic bacterial groups.
Genetic Evidence Suggests that the Intergenic Region between
pstA
and
pstB
Plays a Role in the Regulation of
rpoS
Translation during Phosphate Limitation
Authors: Schurdell Michael S. , Woodbury Garrett M. , McCleary William R. 
Published: December 2006

ABSTRACT

In addition to the Pho regulon, phosphate starvation also stimulates the accumulation of RpoS. Several deletion mutations within the
pstSCAB-phoU
operon were tested for the accumulation of RpoS during exponential growth. Our data suggest that the processed 3′ end of the
pstA
message stimulates translation of
rpoS
.
Does the Importance of the C-Terminal Residues in the Maturation of RgpB from
Porphyromonas gingivalis
Reveal a Novel Mechanism for Protein Export in a Subgroup of Gram-Negative Bacteria?
Authors: Nguyen Ky-Anh , Travis James , Potempa Jan 
Published: December 2006

ABSTRACT

The mature 507-residue RgpB protein belongs to an important class of extracellular outer membrane-associated proteases, the gingipains, from the oral pathogen
Porphyromonas gingivalis
that has been shown to play a central role in the virulence of the organism. The C termini of these gingipains along with other outer membrane proteins from the organism share homologous sequences and have been suggested to function in attachment of these proteins to the outer membrane. In this report, we have created a series of truncated and site-directed mutants of the C terminus from a representative member of this class, the RgpB protease, to investigate its role in the maturation of these proteins. Truncation of the last two residues (valyl-lysine) from the C terminus is sufficient to create an inactive version of the protein that lacks the posttranslational glycosylation seen in the wild type, and the protein remains trapped behind the outer membrane. Alanine scanning of the last five residues revealed the importance of the C-terminal motif in mediating correct posttranslational modification of the protein. This result may have a wider implication in a novel secretory pathway in distinct members of the
Cytophaga-Flavobacterium-Bacteroidetes
phylum.
Interaction of GapA with HPr and Its Homologue, Crh: Novel Levels of Regulation of a Key Step of Glycolysis inBacillus subtilis?
Authors: Pompeo Frédérique , Luciano Jennifer , Galinier Anne 
Published: December 2006

ABSTRACTInBacillus subtiliscells, we identified a new partner of HPr, an enzyme of the glycolysis pathway, the glyceraldehyde-3-phosphate dehydrogenase GapA. We showed that, in vitro, phosphorylated and unphosphorylated forms of HPr and its homologue, Crh, could interact with GapA, but only their seryl-phosphorylated forms were able to inhibit its activity.
Chloroplast SecA and
Escherichia coli
SecA Have Distinct Lipid and Signal Peptide Preferences
Authors: Sun Changqi , Rusch Sharyn L. , Kim Jinoh , Kendall Debra A. 
Published: December 2006

ABSTRACT

Like prokaryotic Sec-dependent protein transport, chloroplasts utilize SecA. However, we observe distinctive requirements for the stimulation of chloroplast SecA ATPase activity; it is optimally stimulated in the presence of galactolipid and only a small fraction of anionic lipid and by Sec-dependent thylakoid signal peptides but not
Escherichia coli
signal peptides.
Histone Deacetylase (HDAC) Inhibitor LBH589 Increases Duration of γ-H2AX Foci and Confines HDAC4 to the Cytoplasm in Irradiated Non–Small Cell Lung Cancer
Authors: Geng Ling , Cuneo Kyle C. , Fu Allie , Tu Tianxiang , Atadja Peter W. , Hallahan Dennis E. 
Published: December 2006

AbstractHistone deacetylases (HDAC) have been identified as therapeutic targets due to their regulatory function in DNA structure and organization. LBH589 is a novel inhibitor of class I and II HDACs. We studied the effect of LBH589 and ionizing radiation (IR) on DNA repair in two human non–small cell lung cancer (NSCLC) cell lines (H23 and H460). γ-H2AX foci present at DNA double-strand breaks (DSBs) were detected in the nuclei following 3 Gy irradiation for up to 6 hours. LBH589 administered before irradiation increased the duration of γ-H2AX foci beyond 24 hours. Furthermore, radiation alone induced translocation of HDAC4 to the nucleus. In contrast, treatment with LBH589 followed by irradiation resulted in HDAC4 confinement to the cytoplasm, indicating that HDAC inhibition affects the nuclear localization of HDAC4. The findings that LBH589 confines HDAC4 to the cytoplasm and increases the duration of γ-H2AX foci in irradiated cell lines suggest that HDAC4 participates in DNA damage signaling following IR. Annexin-propidium iodide flow cytometry assays, cell morphology studies, and cleaved caspase-3 Western blot analysis revealed a synergistic effect of LBH589 with IR in inducing apoptosis. Clonogenic survival showed a greater than additive effect when LBH589 was administered before irradiation compared with irradiation alone. In vivo tumor volume studies showed a growth delay of 20 days with combined treatment compared with 4 and 2 days for radiation or LBH589 alone. This study identifies HDAC4 as a biomarker of LBH589 activity and recognizes the ability of LBH589 to sensitize human NSCLC to radiation-induced DNA DSBs. (Cancer Res 2006; 66(23): 11298-304)
Androgen Receptor Coactivators Lysine-Specific Histone Demethylase 1 and Four and a Half LIM Domain Protein 2 Predict Risk of Prostate Cancer Recurrence
Authors: Kahl Philip , Gullotti Lucia , Heukamp Lukas Carl , Wolf Susanne , Friedrichs Nicolaus , Vorreuther Roland , Solleder Gerold , Bastian Patrick J. , Ellinger Jörg , Metzger Eric , Schüle Roland , Buettner Reinhard 
Published: December 2006

Abstract
Prostate cancer biology varies from locally confined tumors with low risk for relapse to tumors with high risk for progression even after radical prostatectomy. Currently, there are no reliable biomarkers to predict tumor relapse and poor clinical outcome. In this study, we correlated expression patterns of the androgen receptor (AR) coactivators lysine-specific histone demethylase 1 (LSD1) and four and a half LIM-domain protein 2 (FHL2), AR, Gleason score, Gleason grade, and p53 expression in clinically organ confined prostate cancers with relapse after radical prostatectomy. Our data reveal that high levels of LSD1, nuclear expression of the FHL2 coactivator, high Gleason score and grade, and very strong staining of nuclear p53 correlate significantly with relapse during follow-up. No correlation exists with relapse and the expression of AR and cytoplasmic expression of FHL2. To confirm these data, we did quantitative reverse transcription-PCR and Western blot analyses in a subset of tumor specimens. Consistently, both LSD1 mRNA and protein levels were significantly up-regulated in high-risk tumors. We previously identified LSD1 and FHL2 as nuclear cofactors interacting specifically with the AR in prostate cells and showed that both stimulate androgen-dependent gene transcription. Our present study suggests that LSD1 and nuclear FHL2 may serve as novel biomarkers predictive for prostate cancer with aggressive biology and point to a role of LSD1 and FHL2 in constitutive activation of AR-mediated growth signals. (Cancer Res 2006; 66(23): 11341-7)
A Novel BH3 Mimetic Reveals a Mitogen-Activated Protein Kinase–Dependent Mechanism of Melanoma Cell Death Controlled by p53 and Reactive Oxygen Species
Authors: Verhaegen Monique , Bauer Joshua A. , Martín de la Vega Cristina , Wang Guoping , Wolter Keith G. , Brenner J. Chadwick , Nikolovska-Coleska Zaneta , Bengtson Audrey , Nair Rajan , Elder James T. , Van Brocklin Matt , Carey Thomas E. , Bradford Carol R. , Wang Shaomeng , Soengas María S. 
Published: December 2006

Abstract
The RAS/BRAF/MEK/ERK mitogen-activated protein kinase (MAPK) pathway is emerging as a key modulator of melanoma initiation and progression. However, a variety of clinical studies indicate that inhibiting the MAPK pathway is insufficient per se to effectively kill melanoma cells. Here, we report on a genetic and pharmacologic approach to identify survival factors responsible for the resistance of melanoma cells to MEK/ERK antagonists. In addition, we describe a new tumor cell–selective means to bypass this resistance in vitro and in vivo. By generating a panel of isogenic cell lines with specific defects in the apoptotic machinery, we found that the ability of melanoma cells to survive in the absence of functional MEK relies on an ERK-independent expression of the antiapoptotic factor Mcl-1 (and to a lesser extent, Bcl-xL and Bcl-2). Using computer-based modeling, we developed a novel Bcl-2 homology domain 3 (BH3) mimetic. This compound, named TW-37, is the first rationally designed small molecule with high affinity for Mcl-1, Bcl-xL, and Bcl-2. Mechanistic analyses of the mode of action of TW-37 showed a synergistic tumor cell killing in the presence of MEK inhibitors. Importantly, TW-37 unveiled an unexpected role of the MAPK pathway in the control of reactive oxygen species (ROS). This function was critical to prevent the activation of proapoptotic functions of p53 in melanoma cells, but surprisingly, it was dispensable for normal melanocytes. Our results suggest that this MAPK-dependent ROS/p53 feedback loop is a point of vulnerability of melanoma cells that can be exploited for rational drug design. (Cancer Res 2006; 66(23): 11348-59)