bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Type IV-Secretion-Like System Is Required for Conjugative DNA Transport of Broad-Host-Range Plasmid pIP501 in Gram-Positive Bacteria
Authors: Abajy Mohammad Y. , Kopeć Jolanta , Schiwon Katarzyna , Burzynski Michal , Döring Mike , Bohn Christine , Grohmann Elisabeth 
Published: January 2007

ABSTRACT

Plasmid pIP501 has a very broad host range for conjugative transfer among a wide variety of gram-positive bacteria and gram-negative
Escherichia coli
. Functionality of the pIP501 transfer (
tra
) genes in
E. coli
was proven by pIP501 retrotransfer to
Enterococcus faecalis
(B. Kurenbach, C. Bohn, J. Prabhu, M. Abudukerim, U. Szewzyk, and E. Grohmann, Plasmid
50:
86-93, 2003). The 15 pIP501
tra
genes are organized in a single operon (B. Kurenbach, J. Kopeć, M. Mägdefrau, K. Andreas, W. Keller, C. Bohn, M. Y. Abajy, and E. Grohmann, Microbiology
152:
637-645, 2006). The pIP501
tra
operon is negatively autoregulated at the transcriptional level by the conjugative DNA relaxase TraA. Three of the 15 pIP501-encoded Tra proteins show significant sequence similarity to the
Agrobacterium
type IV secretion system proteins VirB1, VirB4, and VirD4. Here we report a comprehensive protein-protein interaction map of all of the pIP501-encoded Tra proteins determined by the yeast two-hybrid assay. Most of the interactions were verified in vitro by isolation of the protein complexes with pull-down assays. In conjunction with known or postulated functions of the pIP501-encoded Tra proteins and computer-assisted prediction of their cellular location, we propose a model for the first type IV-secretion-like system encoded by a conjugative plasmid from gram-positive bacteria.
Porins Are Required for Uptake of Phosphates by
Mycobacterium smegmatis
Authors: Wolschendorf Frank , Mahfoud Maysa , Niederweis Michael 
Published: January 2007

ABSTRACT

Phosphorus is an essential nutrient, but how phosphates cross the mycobacterial cell wall is unknown. Phosphatase activity in whole cells of
Mycobacterium smegmatis
was significantly lower than that in lysed cells, indicating that access to the substrate was restricted. The loss of the outer membrane (OM) porin MspA also reduced the phosphatase activity in whole cells compared to that in lysed cells. A similar result was obtained for
M. smegmatis
that overexpressed endogenous alkaline phosphatase, indicating that PhoA is not a surface protein, contrary to a previous report. The uptake of phosphate by a mutant lacking the porins MspA and MspC was twofold lower than that by wild-type
M. smegmatis
. Strikingly, the loss of these porins resulted in a severe growth defect of
M. smegmatis
on low-phosphate plates. We concluded that the OM of
M. smegmatis
represents a permeability barrier for phosphates and that Msp porins are the only OM channels for the diffusion of phosphate in
M. smegmatis
. However, phosphate diffusion through Msp pores is rather inefficient as shown by the 10-fold lower permeability of
M. smegmatis
for phosphate compared to that for glucose. This is likely due to the negative charges in the constriction zone of Msp porins. The phosphatase activity in whole cells of
Mycobacterium bovis
BCG was significantly less than that in lysed cells, indicating a similar uptake pathway for phosphates in slow-growing mycobacteria. However, porins that could mediate the diffusion of phosphates across the OM of
M. bovis
BCG and
Mycobacterium tuberculosis
are unknown.
The Novel Transcription Factor SgrR Coordinates the Response to Glucose-Phosphate Stress
Authors: Vanderpool Carin K. , Gottesman Susan 
Published: January 2007

ABSTRACT

SgrR is the first characterized member of a family of bacterial transcription factors containing an N-terminal DNA binding domain and a C-terminal solute binding domain. Previously, we reported genetic evidence that SgrR activates the divergently transcribed gene
sgrS
, which encodes a small RNA required for recovery from glucose-phosphate stress. In this study, we examined the regulation of
sgrR
expression and found that SgrR negatively autoregulates its own transcription in the presence and absence of stress. An SgrR binding site in the
sgrR-sgrS
intergenic region is required in vivo for both SgrR-dependent activation of
sgrS
and autorepression of
sgrR
. Purified SgrR binds specifically to
sgrS
promoter DNA in vitro; a mutation in the site required for in vivo activation and autorepression abrogates in vitro SgrR binding. A plasmid library screen identified clones that alter expression of a P

sgrS

-lacZ
fusion; some act by titrating endogenous SgrR. The
yfdZ
gene, encoding a putative aminotransferase, was identified in this screen; the
yfdZ
promoter contains an SgrR binding site, and transcriptional fusions indicate that
yfdZ
is activated by SgrR. Clones containing
mlc
, which encodes a glucose-specific repressor protein, also downregulate P

sgrS

-lacZ
. The
mlc
clones do not appear to titrate the SgrR protein, indicating that Mlc affects
sgrS
expression by an alternative mechanism.
Cytological Analysis of the Mother Cell Death Process during Sporulation in
Bacillus subtilis
Authors: Hosoya Shigeo , Lu Zuolei , Ozaki Yousuke , Takeuchi Michio , Sato Tsutomu 
Published: January 2007

ABSTRACT

We have identified the following events during the late stage in the mother cell in
Bacillus subtilis
: spore detachment from the polar site of the mother cell, membrane rupture, cell wall collapse, and release of the free spore. The membrane rupture was followed by mother cell lysis. Moreover, we found that NucB, an extracellular nuclease, is involved in DNA degradation after mother cell lysis.
Sinorhizobium meliloti
SyrA Mediates the Transcriptional Regulation of Genes Involved in Lipopolysaccharide Sulfation and Exopolysaccharide Biosynthesis
Authors: Keating David H. 
Published: January 2007

ABSTRACT

Sinorhizobium meliloti
is a gram-negative soil bacterium found either in free-living form or as a nitrogen-fixing endosymbiont of leguminous plants such as
Medicago sativa
(alfalfa).
S. meliloti
synthesizes an unusual sulfate-modified form of lipopolysaccharide (LPS). A recent study reported the identification of a gene,
lpsS
, which encodes an LPS sulfotransferase activity in
S. meliloti
. Mutants bearing a disrupted version of
lpsS
exhibit an altered symbiosis, in that they elicit more nodules than wild type. However, under free-living conditions, the
lpsS
mutant displayed no change in LPS sulfation. These data suggest that the expression of
lpsS
is differentially regulated, such that it is transcriptionally repressed during free-living conditions but upregulated during symbiosis. Here, I show that the expression of
lpsS
is upregulated in strains that constitutively express the symbiotic regulator SyrA. SyrA is a small protein that lacks an apparent DNA binding domain and is predicted to be located in the cytoplasmic membrane yet is sufficient to upregulate
lpsS
transcription. Furthermore, SyrA can mediate the transcriptional upregulation of
exo
genes involved in the biosynthesis of the symbiotic exopolysaccharide succinoglycan. The SyrA-mediated transcriptional upregulation of
lpsS
and
exo
transcription is blocked in mutants harboring a mutation in
chvI
, which encodes the response regulator of a conserved two-component system. Thus, SyrA likely acts indirectly to promote transcriptional upregulation of
lpsS
and
exo
genes through a mechanism that requires the ExoS/ChvI two-component system.
Presence or Absence of Lipopolysaccharide O Antigens Affects Type III Secretion by
Pseudomonas aeruginosa
Authors: Augustin D. K. , Song Y. , Baek M. S. , Sawa Y. , Singh G. , Taylor B. , Rubio-Mills A. , Flanagan J. L. , Wiener-Kronish J. P. , Lynch S. V. 
Published: January 2007

ABSTRACT

Pseudomonas aeruginosa
is one of the major causative agents of mortality and morbidity in hospitalized patients due to a multiplicity of virulence factors associated with both chronic and acute infections. Acute
P. aeruginosa
infection is primarily mediated by planktonic bacteria expressing the type III secretion system (TTSS), a surface-attached needle-like complex that injects cytotoxins directly into eukaryotic cells, causing cellular damage. Lipopolysaccharide (LPS) is the principal surface-associated virulence factor of
P. aeruginosa
. This molecule is known to undergo structural modification (primarily alterations in the A- and B-band O antigen) in response to changes in the mode of life (e.g., from biofilm to planktonic). Given that LPS exhibits structural plasticity, we hypothesized that the presence of LPS lacking O antigen would facilitate eukaryotic intoxication and that a correlation between the LPS O-antigen serotype and TTSS-mediated cytotoxicity would exist. Therefore, strain PAO1 (A
+
B
+
O-antigen serotype) and isogenic mutants with specific O-antigen defects (A
+
B
−
, A
−
B
+
, and A
−
B
−
) were examined for TTSS expression and cytotoxicity. A strong association existed in vitro between the absence of the large, structured B-band O antigen and increased cytotoxicity of these strains. In vivo, all three LPS mutant strains demonstrated significantly increased lung injury compared to PAO1. Clinical strains lacking the B-band O antigen also demonstrated increased TTSS secretion. These results suggest the existence of a cooperative association between LPS O-antigen structure and the TTSS in both laboratory and clinical isolates of
P. aeruginosa
.
Genome Sequence and Analysis of the Soil Cellulolytic ActinomyceteThermobifida fuscaYX
Authors: Lykidis Athanasios , Mavromatis Konstantinos , Ivanova Natalia , Anderson Iain , Land Miriam , DiBartolo Genevieve , Martinez Michele , Lapidus Alla , Lucas Susan , Copeland Alex , Richardson Paul , Wilson David B. , Kyrpides Nikos 
Published: January 2007

ABSTRACTThermobifida fuscais a moderately thermophilic soil bacterium that belongs toActinobacteria. It is a major degrader of plant cell walls and has been used as a model organism for the study of secreted, thermostable cellulases. The complete genome sequence showed thatT. fuscahas a single circular chromosome of 3,642,249 bp predicted to encode 3,117 proteins and 65 RNA species with a coding density of 85%. Genome analysis revealed the existence of 29 putative glycoside hydrolases in addition to the previously identified cellulases and xylanases. The glycosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch- and xylan-degrading functions.T. fuscapossesses two protein secretion systems: thesecgeneral secretion system and the twin-arginine translocation system. Several of the secreted cellulases have sequence signatures indicating their secretion may be mediated by the twin-arginine translocation system.T. fuscahas extensive transport systems for import of carbohydrates coupled to transcriptional regulators controlling the expression of the transporters and glycosylhydrolases. In addition to providing an overview of the physiology of a soil actinomycete, this study presents insights on the transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems.
Nitric Oxide in Physiologic Concentrations Targets the Translational Machinery to Increase the Proliferation of Human Breast Cancer Cells: Involvement of Mammalian Target of Rapamycin/eIF4E Pathway
Authors: Pervin Shehla , Singh Rajan , Hernandez Estebes , Wu Guoyao , Chaudhuri Gautam 
Published: January 2007

Abstract
Nitric oxide (NO) in nanomolar (nmol/L) concentrations is consistently detected in tumor microenvironment and has been found to promote tumorigenesis. The mechanism by which NO enhances tumor progression is largely unknown. In this study, we investigated the possible mechanisms and identified cellular targets by which NO increases proliferation of human breast cancer cell lines MDA-MB-231 and MCF-7. DETA-NONOate, a long acting NO donor, with a half-life of 20 h, was used. We found that NO (nmol/L) dramatically increased total protein synthesis in MDA-MB-231 and MCF-7 and also increased cell proliferation. NO specifically increased the translation of cyclin D1 and ornithine decarboxylase (ODC) without altering their mRNA levels or half-lives. Critical components in the translational machinery, such as phosphorylated mammalian target of rapamycin (mTOR) and its downstream targets, phosphorylated eukaryotic translation initiation factor and p70 S6 kinase, were up-regulated following NO treatment, and inhibition of mTOR with rapamycin attenuated NO induced increase of cyclin D1 and ODC. Activation of translational machinery was mediated by NO-induced up-regulation of the Raf/mitogen-activated protein/extracellular signal-regulated kinase (ERK) kinase/ERK (Raf/MEK/ERK) and phosphatidylinositol 3-kinase (PI-3 kinase)/Akt signaling pathways. Up-regulation of the Raf/MEK/ERK and PI-3 kinase/Akt pathways by NO was found to be mediated by activation of Ras, which was cyclic guanosine 3′,5′-monophosphate independent. Furthermore, inactivation of Ras by farnesyl transferase inhibitor or K-Ras small interfering RNA attenuated NO-induced increase in proliferation signaling and cyclin D1 and ODC translation, further confirming the involvement of Ras activation during NO-induced cell proliferation. [Cancer Res 2007;67(1):289–99]
Allelic Loss in a Minimal Region on Chromosome 16q24 Is Associated with Vitreous Seeding of Retinoblastoma
Authors: Gratias Sandrine , Rieder Harald , Ullmann Reinhard , Klein-Hitpass Ludger , Schneider Stephanie , Bölöni Réka , Kappler Martin , Lohmann Dietmar R. 
Published: January 2007

Abstract
In addition to RB1 gene mutations, retinoblastomas frequently show gains of 1q and 6p and losses of 16q. To identify suppressor genes on 16q, we analyzed 22 short tandem repeat loci in 58 patients with known RB1 mutations. A subset of tumors was also investigated by conventional and matrix comparative genomic hybridization. In 40 of 58 (69%) tumors, we found no loss of heterozygosity (LOH) at any 16q marker. LOH was detected in 18 of 58 (31%) tumors, including five with allelic imbalance at some markers. In one tumor LOH was only observed at 16q24. As the parental origin of allele loss was unbiased, an imprinted locus is unlikely to be involved. Analysis of gene expression by microarray hybridization and quantitative RT real-time PCR did not identify a candidate suppressor in 16q24. Cadherin 13 (CDH13), CBFA2T3, and WFDC1, which are candidate suppressors in other tumor entities with 16q24 loss, did not show loss of expression. In addition, mutation and methylation analysis showed no somatic alteration of CDH13. Results in all tumors with chromosome 16 alterations define a single minimal deleted region of 5.7 Mb in the telomeric part of 16q24 with the centromeric boundary defined by retention of heterozygosity for a single nucleotide variant in exon 10 of CDH13 (Mb 82.7). Interestingly, clinical presentation of tumors with and without 16q alterations was distinct. Specifically, almost all retinoblastomas with 16q24 loss showed diffuse intraocular seeding. This suggests that genetic alterations in the minimal deleted region are associated with impaired cell-to-cell adhesion. [Cancer Res 2007;67(1):408–16]
An Organometallic Protein Kinase Inhibitor Pharmacologically Activates p53 and Induces Apoptosis in Human Melanoma Cells
Authors: Smalley Keiran S.M. , Contractor Rooha , Haass Nikolas K. , Kulp Angela N. , Atilla-Gokcumen G. Ekin , Williams Douglas S. , Bregman Howard , Flaherty Keith T. , Soengas Maria S. , Meggers Eric , Herlyn Meenhard 
Published: January 2007

Abstract
Unlike other tumors, melanomas harbor wild-type (WT) p53 but exhibit impaired p53-dependent apoptosis. The mechanisms for the impaired p53 activation are poorly understood but may be linked to the high expression of the p53 suppressor Mdm2, which is found in &gt;50% of melanoma lesions. Here, we describe an organometallic glycogen synthase kinase 3β (GSK3β) inhibitor (DW1/2) as a potent activator of p53 and inducer of cell death in otherwise highly chemoresistant melanoma cells. Using RNA interference and pharmacologic approaches, we show that p53 is required for the cytotoxic effects of this organometallic inhibitor. The DW1/2 compound was barely able to induce cell death in melanoma cells with p53 mutations, further confirming the requirement for p53-WT in the cytotoxic effects of the GSK3β inhibition. Mechanistic analysis of the p53-dependent cell death indicated an apoptotic mechanism involving depolarization of mitochondrial membrane potential, caspase cleavage, and elevated NOXA expression. The effect of p53 was not simply due to passive up-regulation of protein expression as adenoviral-mediated overexpression of p53 was not able to induce cell death. Treatment of melanoma cells with DW1/2 was instead found to decrease levels of Mdm2 and Mdm4. The importance of Mdm2 down-regulation in DW1/2-induced apoptosis was confirmed by treating the p53-WT cells with the p53/Mdm2 antagonist Nutlin-3. Taken together, our data provide a new strategy for the pharmacologic activation of p53 in melanoma, which may be a viable approach for overcoming apoptotic resistance in melanoma and offer new hope for rational melanoma therapy. [Cancer Res 2007;67(1):209–17]
TRAIL Induces Receptor-Interacting Protein 1–Dependent and Caspase-Dependent Necrosis-Like Cell Death under Acidic Extracellular Conditions
Authors: Meurette Olivier , Rebillard Amélie , Huc Laurence , Le Moigne Gwenaëlle , Merino Delphine , Micheau Olivier , Lagadic-Gossmann Dominique , Dimanche-Boitrel Marie-Thérèse 
Published: January 2007

AbstractTumor necrosis factor-α–related apoptosis-inducing ligand (TRAIL) is a potential anticancer agent that induces apoptosis in cancer cells but not in most normal cells. How tumor physiology, particularly acidic extracellular pH (pHe), would modify sensitivity of cancer cells to TRAIL-induced cell death is not known. We have previously shown that cancer cells, resistant to TRAIL-induced apoptosis at physiologic pHe (7.4), could be sensitized to TRAIL at acidic pHe (6.5). However, at this acidic pHe, cell death was necrotic. We show here that, in spite of a necrosis-like cell death morphology, caspases are activated and are necessary for TRAIL-induced cell death at acidic pHe in HT29 human colon cancer cells. Furthermore, we observed that, whereas receptor-interacting protein (RIP) was cleaved following TRAIL treatment at physiologic pHe (7.4), it was not cleaved following TRAIL treatment at acidic pHe (6.5). Moreover, RIP degradation by geldanamycin or decrease expression of RIP by small RNA interference transfection inhibited TRAIL-induced necrosis at acidic pHe, showing that RIP was necessary for this necrotic cell death pathway. We also show that RIP kinase activity was essential for this cell death pathway. Altogether, we show that, under acidic pHe conditions, TRAIL induces a necrosis-like cell death pathway that depends both on caspases and RIP kinase activity. Thus, our data suggest for the first time that RIP-dependent necrosis might be a major death pathway in TRAIL-based therapy in solid tumors with acidic pHe. [Cancer Res 2007;67(1):218–26]
Inactivated Sendai Virus Particles Eradicate Tumors by Inducing Immune Responses through Blocking Regulatory T Cells
Authors: Kurooka Masayuki , Kaneda Yasufumi 
Published: January 2007

AbstractUV-inactivated, replication-defective Sendai virus particles [hemagglutinating virus of Japan envelope (HVJ-E)] injected into murine colon carcinoma (CT26) tumors growing in syngeneic BALB/c mice eradicated 60% to 80% of the tumors and obviously inhibited the growth of the remainder. Induced adaptive antitumor immune responses were dominant in the tumor eradication process because the effect was abrogated in severe combined immunodeficient mice. Murine and human dendritic cells underwent dose-dependent maturation by HVJ-E in vitro. Profiles of cytokines secreted by dendritic cells after HVJ-E stimulation showed that the amount of interleukin-6 (IL-6) released was comparable to that elicited by live HVJ. Real-time reverse transcription-PCR and immunohistochemistry revealed that HVJ-E induced a remarkable infiltration of dendritic cells and CD4+ and CD8+ T cells into tumors. In addition, CT26-specific CTLs were induced with the evidence of enhanced CD8+ T-cell activation in a CD4+CD25− T cell–dependent manner. On the other hand, conditioned medium from dendritic cells stimulated by HVJ-E rescued CD4+CD25− effector T-cell proliferation from Foxp3+CD4+CD25+ regulatory T cell (Treg)–mediated suppression and IL-6 was presumably dominant for this phenomenon. We also confirmed such rescue in mice treated with HVJ-E in vivo. Moreover, antitumor effect of HVJ-E was significantly reduced by an in vivo blockade of IL-6 signaling. This is the first report to show that HVJ-E alone can eradicate tumors and the mechanism through which it induces antitumor immune responses. Because it can enhance antitumor immunity and simultaneously remove Treg-mediated suppression, HVJ-E shows promise as a novel therapeutic for cancer immunotherapy. [Cancer Res 2007;67(1):227–36]
Daxx Cooperates with the Axin/HIPK2/p53 Complex to Induce Cell Death
Authors: Li Qinxi , Wang Xuan , Wu Xiaoling , Rui Yanning , Liu Wei , Wang Jifeng , Wang Xinghao , Liou Yih-Cherng , Ye Zhiyun , Lin Sheng-Cai 
Published: January 2007

Abstract
Daxx, a death domain–associated protein, has been implicated in proapoptosis, antiapoptosis, and transcriptional regulation. Many factors known to play critically important roles in controlling apoptosis and gene transcription have been shown to associate with Daxx, including the Ser/Thr protein kinase HIPK2, promyelocytic leukemia protein, histone deacetylases, and the chromatin remodeling protein ATRX. Although it is clear that Daxx may exert multiple functions, the underlying mechanisms remain far from clear. Here, we show that Axin, originally identified for its scaffolding role to control β-catenin levels in Wnt signaling, strongly associates with Daxx at endogenous levels. The Daxx/Axin complex formation is enhanced by UV irradiation. Axin tethers Daxx to the tumor suppressor p53, and cooperates with Daxx, but not DaxxΔAxin, which is unable to interact with Axin, to stimulate HIPK2-mediated Ser46 phosphorylation and transcriptional activity of p53. Interestingly, Axin and Daxx seem to selectively activate p53 target genes, with strong activation of PUMA, but not p21 or Bax. Daxx-stimulated p53 transcriptional activity was significantly diminished by small interfering RNA against Axin; Daxx fails to inhibit colony formation in Axin−/− cells. Moreover, UV-induced cell death was attenuated by the knockdown of Axin and Daxx. All these results show that Daxx cooperates with Axin to stimulate p53, and implicate a direct role for Axin, HIPK2, and p53 in the proapoptotic function of Daxx. We have hence unraveled a novel aspect of p53 activation and shed new light on the ultimate understanding of the Daxx protein, perhaps most pertinently, in relation to stress-induced cell death. [Cancer Res 2007;67(1):66–74]