bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divergent Regulatory Pathways Control A and S Motility in
Myxococcus xanthus
through FrzE, a CheA-CheY Fusion Protein
Authors: Li Yinuo , Bustamante Víctor H. , Lux Renate , Zusman David , Shi Wenyuan 
Published: February 2005

ABSTRACT

Myxococcus xanthus
moves on solid surfaces by using two gliding motility systems, A motility for individual-cell movement and S motility for coordinated group movements. The
frz
genes encode chemotaxis homologues that control the cellular reversal frequency of both motility systems. One of the components of the core Frz signal transduction pathway, FrzE, is homologous to both CheA and CheY from the enteric bacteria and is therefore a novel CheA-CheY fusion protein. In this study, we investigated the role of this fusion protein, in particular, the CheY domain (FrzE
CheY
). FrzE
CheY
retains all of the highly conserved residues of the CheY superfamily of response regulators, including Asp709, analogous to phosphoaccepting Asp57 of
Escherichia coli
CheY. While in-frame deletion of the entire
frzE
gene caused both motility systems to show a hyporeversal phenotype, in-frame deletion of the FrzE
CheY
domain resulted in divergent phenotypes for the two motility systems: hyperreversals of the A-motility system and hyporeversals of the S-motility system. To further investigate the role of FrzE
CheY
in A and S motility, point mutations were constructed such that the putative phosphoaccepting residue, Asp709, was changed from D to A (and was therefore never subject to phosphorylation) or E (possibly mimicking constitutive phosphorylation). The D709A mutant showed hyperreversals for both motilities, while the D709E mutant showed hyperreversals for A motility and hyporeversal for S motility. These results show that the FrzE
CheY
domain plays a critical signaling role in coordinating A and S motility. On the basis of the phenotypic analyses of the
frzE
mutants generated in this study, a model is proposed for the divergent signal transduction through FrzE in controlling and coordinating A and S motility in
M. xanthus
.
Multiple Extracellular Loops Contribute to Substrate Binding and Transport by the
Escherichia coli
Cobalamin Transporter BtuB
Authors: Fuller-Schaefer Cynthia A. , Kadner Robert J. 
Published: February 2005

ABSTRACT

The
Escherichia coli
outer membrane TonB-dependent transporters for iron complexes and cobalamins recognize their multiple and diverse substrates with high specificity and affinity. The X-ray crystallographic structures of several transporters show that the substrate-binding surfaces are comprised of residues from the internal globular domain and multiple extracellular loops. The extracellular loops on the N-terminal half of the transmembrane beta-barrel of the cobalamin transporter BtuB participate in binding of the cofactor calcium atoms and undergo substantial conformation changes upon substrate binding. The functional relevance of the five C-terminal loops was examined by examining the effects of short in-frame deletions. Each loop contributed in different ways to the binding of BtuB substrates. Deletions in loops 7, 8, 9, and 11 strongly decreased cobalamin binding and transport, whereas deletions in loops 8, 9, and 10 affected binding and entry of phage BF23. None of the loops were essential for the action of colicin E1 or E3, which is consistent with the crystallographic observation that the colicin E3 receptor-binding domain can contact almost all of the loops. A deletion in loop 9 or 11 eliminated the ability of cobalamin to inhibit the action of colicin E1. These phenotypes show that there are multiple independent binding elements and point out similarities and differences in binding properties among the TonB-dependent transporters.
Genome-Wide Analyses of
Escherichia coli
Gene Expression Responsive to the BaeSR Two-Component Regulatory System
Authors: Nishino Kunihiko , Honda Takeshi , Yamaguchi Akihito 
Published: February 2005

ABSTRACT

The BaeSR two-component regulatory system controls expression of exporter genes conferring drug resistance in
Escherichia coli
(S. Nagakubo, K. Nishino, T. Hirata, and A. Yamaguchi, J. Bacteriol.
184:
4161-4167, 2002; N. Baranova and H. Nikaido, J. Bacteriol.
184:
4168-4176, 2002). To understand the whole picture of BaeSR regulation, a DNA microarray analysis of the effect of BaeR overproduction was performed. BaeR overproduction activated 59 genes related to two-component signal transduction, chemotactic responses, flagellar biosynthesis, maltose transport, and multidrug transport, and BaeR overproduction also repressed the expression of the
ibpA
and
ibpB
genes. All of the changes in the expression levels were also observed by quantitative real-time reverse transcription-PCR analysis. The expression levels of 15 of the 59 BaeR-activated genes were decreased by deletion of
baeSR
. Of 11 genes induced by indole (a putative inducer of the BaeSR system), 10 required the BaeSR system for induction. Combination of the expression data sets revealed a BaeR-binding site sequence motif, 5′-TTTTTCTCCATDATTGGC-3′ (where D is G, A, or T). Several genes up-regulated by BaeR overproduction, including genes for maltose transport, chemotactic responses, and flagellar biosynthesis, required an intact PhoBR or CreBC two-component regulatory system for up-regulation. These data indicate that there is cross-regulation among the BaeSR, PhoBR, and CreBC two-component regulatory systems. Such a global analysis should reveal the regulatory network of the BaeSR system.
Structure of the Nucleotide Complex of PyrR, the
pyr
Attenuation Protein from
Bacillus caldolyticus
, Suggests Dual Regulation by Pyrimidine and Purine Nucleotides
Authors: Chander Preethi , Halbig Kari M. , Miller Jamie K. , Fields Christopher J. , Bonner Heather K. S. , Grabner Gail K. , Switzer Robert L. , Smith Janet L. 
Published: February 2005

ABSTRACT

PyrR is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (
pyr
genes) in many bacteria. PyrR acts by binding to specific sequences on
pyr
mRNA and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. PyrR from
Bacillus subtilis
has been purified and extensively studied. In this work, we describe the purification to homogeneity and characterization of recombinant PyrR from the thermophile
Bacillus caldolyticus
and the crystal structures of unliganded PyrR and a PyrR-nucleotide complex. The
B. caldolyticus pyrR
gene was previously shown to restore normal regulation of the
B. subtilis pyr
operon in a
pyrR
deletion mutant. Like
B. subtilis
PyrR,
B. caldolyticus
PyrR catalyzes the uracil phosphoribosyltransferase reaction but with maximal activity at 60°C. Crystal structures of
B. caldolyticus
PyrR reveal a dimer similar to the
B. subtilis
PyrR dimer and, for the first time, binding sites for nucleotides. UMP and GMP, accompanied by Mg
2+
, bind specifically to PyrR active sites. Nucleotide binding to PyrR is similar to other phosphoribosyltransferases, but Mg
2+
binding differs. GMP binding was unexpected. The protein bound specific sequences of
pyr
RNA 100 to 1,000 times more tightly than
B. subtilis
PyrR, depending on the RNA tested and the assay method; uridine nucleotides enhanced RNA binding, but guanosine nucleotides antagonized it. The new findings of specific GMP binding and its antagonism of RNA binding suggest cross-regulation of the
pyr
operon by purines.
Screening for Quorum-Sensing Inhibitors (QSI) by Use of a Novel Genetic System, the QSI Selector
Authors: Rasmussen Thomas Bovbjerg , Bjarnsholt Thomas , Skindersoe Mette Elena , Hentzer Morten , Kristoffersen Peter , Köte Manuela , Nielsen John , Eberl Leo , Givskov Michael 
Published: February 2005

ABSTRACT

With the widespread appearance of antibiotic-resistant bacteria, there is an increasing demand for novel strategies to control infectious diseases. Furthermore, it has become apparent that the bacterial life style also contributes significantly to this problem. Bacteria living in the biofilm mode of growth tolerate conventional antimicrobial treatments. The discovery that many bacteria use quorum-sensing (QS) systems to coordinate virulence and biofilm development has pointed out a new, promising target for antimicrobial drugs. We constructed a collection of screening systems, QS inhibitor (QSI) selectors, which enabled us to identify a number of novel QSIs among natural and synthetic compound libraries. The two most active were garlic extract and 4-nitro-pyridine-
N
-oxide (4-NPO). GeneChip-based transcriptome analysis revealed that garlic extract and 4-NPO had specificity for QS-controlled virulence genes in
Pseudomonas aeruginosa
. These two QSIs also significantly reduced
P. aeruginosa
biofilm tolerance to tobramycin treatment as well as virulence in a
Caenorhabditis elegans
pathogenesis model.
Role of Penicillin-Binding Protein 2 (PBP2) in the Antibiotic Susceptibility and Cell Wall Cross-Linking of
Staphylococcus aureus
: Evidence for the Cooperative Functioning of PBP2, PBP4, and PBP2A
Authors: Łęski Tomasz A. , Tomasz Alexander 
Published: February 2005

ABSTRACT

Ceftizoxime, a beta-lactam antibiotic with high selective affinity for penicillin-binding protein 2 (PBP2) of
Staphylococcus aureus
, was used to select a spontaneous resistant mutant of
S. aureus
strain 27s. The stable resistant mutant ZOX3 had an increased ceftizoxime MIC and a decreased affinity of its PBP2 for ceftizoxime and produced peptidoglycan in which the proportion of highly cross-linked muropeptides was reduced. The
pbpB
gene of ZOX3 carried a single C-to-T nucleotide substitution at nucleotide 1373, causing replacement of a proline with a leucine at amino acid residue 458 of the transpeptidase domain of the protein, close to the SFN conserved motif. Experimental proof that this point mutation was responsible for the drug-resistant phenotype, and also for the decreased PBP2 affinity and reduced cell wall cross-linking, was provided by allelic replacement experiments and site-directed mutagenesis. Disruption of
pbpD
, the structural gene of PBP4, in either the parental strain or the mutant caused a large decrease in the highly cross-linked muropeptide components of the cell wall and in the mutant caused a massive accumulation of muropeptide monomers as well. Disruption of
pbpD
also caused increased sensitivity to ceftizoxime in both the parental cells and the ZOX3 mutant, while introduction of the plasmid-borne
mecA
gene, the genetic determinant of the beta-lactam resistance protein PBP2A, had the opposite effects. The findings provide evidence for the cooperative functioning of two native
S. aureus
transpeptidases (PBP2 and PBP4) and an acquired transpeptidase (PBP2A) in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents.
Light-Induced Carotenogenesis inStreptomyces coelicolorA3(2): Identification of an Extracytoplasmic Function Sigma Factor That Directs Photodependent Transcription of the Carotenoid Biosynthesis Gene Cluster
Authors: Takano Hideaki , Obitsu Saemi , Beppu Teruhiko , Ueda Kenji 
Published: February 2005

ABSTRACTCarotenoids are produced by a variety of organisms, but the mechanisms that regulate gene expression leading to carotenoid biosynthesis have been characterized for only a few organisms. In this study, we found thatStreptomyces coelicolorA3(2), a gram-positive filamentous bacterium, produces carotenoids under blue light induction. The carotenoid fraction isolated from the cell extract contained multiple compounds, including isorenieratene and β-carotene. The carotenoid biosynthesis gene cluster ofS. coelicolorconsists of two convergent operons,crtEIBVandcrtYTU, as previously shown forStreptomyces griseus. ThecrtEIBVnull mutant completely lost its ability to produce carotenoids. Thecrtgene cluster is flanked by a regulatory region that consists of two divergent operons,litRQandlitSAB. Thelit(light-induced transcription) genes encode a MerR-type transcriptional regulator (LitR), a possible oxidoreductase (LitQ), an extracytoplasmic function sigma factor (σLitS), a putative lipoprotein (LitA), and a putative anti-sigma factor (LitB). S1 protection assay revealed that the promoters precedingcrtE(PcrtE),crtY(PcrtY),litR(PlitR), andlitS(PlitS) are activated upon illumination. AlitSmutant lost both the ability to produce carotenoids and the activities of PcrtE, PcrtY, and PlitS, which suggested that σLitSdirects light-induced transcription from these promoters. An RNA polymerase holocomplex containing purified σLitSrecombinant protein generated specific PcrtEand PcrtYtranscripts in an in vitro runoff transcriptional assay. AlitRmutant that had an insertion of the kanamycin resistance gene was defective both in the ability to produce carotenoids and in all of the light-dependent promoter activities. Overexpression oflitSresulted in constitutive carotenoid production in both the wild type and thelitRmutant. These results indicate that σLitSacts as a light-induced sigma factor that directs transcription of thecrtbiosynthesis gene cluster, whose activity is controlled by an unknown LitR function. This is the first report to describe light-inducible gene expression inStreptomyces.
DNA Bridging: a Property Shared among H-NS-Like Proteins
Authors: Dame Remus T. , Luijsterburg Martijn S. , Krin Evelyne , Bertin Philippe N. , Wagner Rolf , Wuite Gijs J. L. 
Published: February 2005

ABSTRACT

The nucleoid-associated protein H-NS is thought to play an essential role in the organization of bacterial chromatin in
Escherichia coli
. Homologues, often with very low sequence identity, are found in most gram-negative bacteria. Microscopic analysis reveals that, despite limited sequence identity, their structural organization results in similar DNA binding properties.
The Promoter Region Rather than Its Downstream Inverted Repeat Sequence Is Responsible for Low-Level Transcription of the Thermostable Direct Hemolysin-Related Hemolysin (
trh
) Gene of
Vibrio parahaemolyticus
Authors: Nakaguchi Yoshitsugu , Nishibuchi Mitsuaki 
Published: February 2005

ABSTRACT

We determined the transcriptional start site of the thermostable direct hemolysin-related hemolysin gene (
trh
) of
Vibrio parahaemolyticus
by using a PCR-based method and identified the promoter. Mutagenic analysis indicated that the promoter-bearing region rather than its downstream inverted repeat sequence was responsible for the low-revel of
trh
transcription.
DNA Content and Nucleoid Distribution in
Methanothermobacter thermautotrophicus
Authors: Majerník Alan I. , Lundgren Magnus , McDermott Paul , Bernander Rolf , Chong James P. J. 
Published: February 2005

ABSTRACT

Flow cytometry and epifluorescence microscopy results for the euryarchaeon
Methanothermobacter thermautotrophicus
were consistent with filaments containing multiple cells. Filaments of one to four cells contained two to eight nucleoids. Single chromosome-containing cells were not observed. Filaments containing multiple genome copies displayed synchronous DNA replication initiation. Chromosome segregation occurred during replication or rapidly after replication termination.
Involvement of P1 Adhesin in Gliding Motility of
Mycoplasma pneumoniae
as Revealed by the Inhibitory Effects of Antibody under Optimized Gliding Conditions
Authors: Seto Shintaro , Kenri Tsuyoshi , Tomiyama Tetsuo , Miyata Makoto 
Published: February 2005

ABSTRACT

To examine the participation of P1 adhesin in gliding of
Mycoplasma pneumoniae
, we examined the effects of an anti-P1 monoclonal antibody on individual gliding mycoplasmas. The antibody reduced the gliding speed and removed the gliding cells from the glass over time in a concentration-dependent manner but had only a slight effect on nongliding cells, suggesting that the conformational changes of P1 adhesin and its displacement are involved in the gliding mechanism.
Human cytotoxic T lymphocytes with reduced sensitivity to Fas-induced apoptosis
Authors: Dotti Gianpietro , Savoldo Barbara , Pule Martin , Straathof Karin C. , Biagi Ettore , Yvon Eric , Vigouroux Stephane , Brenner Malcolm K. , Rooney Cliona M. 
Published: February 2005

AbstractEffector-memory T cells expressing Fas (Apo-1/CD95) are switched to an apoptotic program by cross-linking with Fas-ligand (FasL). Consequently, tumors that express FasL can induce apoptosis of infiltrating Fas-positive T lymphocytes and subdue any antitumor host immune response. Since Epstein-Barr virus (EBV)-associated tumors such as Hodgkin lymphoma (HL) and nasopharyngeal carcinoma (NPC) express FasL, we determined whether EBV-specific cytotoxic T lymphocytes (EBV-CTLs) could be modified to resist this evasion strategy. We show that long-term down-modulation of Fas can be achieved in EBV-CTLs by transduction with small interfering RNA (siRNA) encoded in a retrovirus. Modified T cells resisted Fas/FasL-mediated apoptosis compared with control cells and showed minimal cleavage of the caspase3 substrate poly(ADP-ribose) polymerase (PARP) protein after Fas engagement. Prolonged Fas stimulation selected a uniformly Faslow and FasL resistant population. Removal of responsiveness to this single death signal had no other discernible effects on EBV-CTLs. In particular, it did not lead to their autonomous growth since the modified EBV-CTLs remained polyclonal, and their survival and proliferation retained dependence on antigen-specific stimulation and on the presence of other physiologic growth signals. EBV-CTLs with knocked down Fas should have a selective functional and survival advantage over unmodified EBV-CTLs in the presence of tumors expressing FasL and may be of value for adoptive cellular therapy. (Blood. 2005;105:4677-4684)
Fusion of EML1 to ABL1 in T-cell acute lymphoblastic leukemia with cryptic t(9;14)(q34;q32)
Authors: De Keersmaecker Kim , Graux Carlos , Odero Maria D. , Mentens Nicole , Somers Riet , Maertens Johan , Wlodarska Iwona , Vandenberghe Peter , Hagemeijer Anne , Marynen Peter , Cools Jan 
Published: February 2005

Abstract
The BCR-ABL1 fusion kinase is frequently associated with chronic myeloid leukemia and B-cell acute lymphoblastic leukemia but is rare in T-cell acute lymphoblastic leukemia (T-ALL). We recently identified NUP214-ABL1 as a variant ABL1 fusion gene in 6% of T-ALL patients. Here we describe the identification of another ABL1 fusion, EML1-ABL1, in a T-ALL patient with a cryptic t(9;14)(q34;q32) associated with deletion of CDKN2A (p16) and expression of TLX1 (HOX11). Echinoderm microtubule-associated protein-like 1-Abelson 1 (EML1-ABL1) is a constitutively phosphorylated tyrosine kinase that transforms Ba/F3 cells to growth factor-independent growth through activation of survival and proliferation pathways, including extracellular signal-related kinase 1/2 (Erk1/2), signal transducers and activators of transcription 5 (Stat5), and Lyn kinase. Deletion of the coiled-coil domain of EML1 abrogated the transforming properties of the fusion kinase. EML1-ABL1 and breakpoint cluster region (BCR)-ABL1 were equally sensitive to the tyrosine kinase inhibitor imatinib. These data further demonstrate the involvement of ABL1 fusions in the pathogenesis of T-ALL and identify EML1-ABL1 as a novel therapeutic target of imatinib. (Blood. 2005;105:4849-4852)
Mammalian cells lack checkpoints for tetraploidy, aberrant centrosome number, and cytokinesis failure
Authors: Wong Connie , Stearns Tim 
Published: February 2005

Abstract
Background
Mammalian cells have been reported to have a p53-dependent tetraploidy checkpoint that blocks cell cycle progression in G1 in response to failure of cell division. In most cases where the tetraploidy checkpoint has been observed cell division was perturbed by anti-cytoskeleton drug treatments. However, other evidence argues against the existence of a tetraploidy checkpoint. Cells that have failed to divide differ from normal cells in having two nuclei, two centrosomes, a decreased surface to volume ratio, and having undergone an abortive cytokinesis. We tested each of these to determine which, if any, cause a G1 cell cycle arrest.

Results
Primary human diploid fibroblasts with intact cell cycle checkpoints were used in all experiments. Synchronized cells exhibited G1 arrest in response to division failure caused by treatment with either cytochalasin or the myosin II inhibitor blebbistatin. The role of tetraploidy, aberrant centrosome number, and increased cell size were tested by cell/cell and cell/cytoplast fusion experiments; none of these conditions resulted in G1 arrest. Instead we found that various drug treatments of the cells resulted in cellular damage, which was the likely cause of the arrest. When cytokinesis was blocked in the absence of damage-inducing drug treatments no G1 arrest was observed.

Conclusions
We show that neither tetraploidy, aberrant centrosome number, cell size, nor failure of cytokinesis lead to G1 arrest, suggesting that there is no tetraploidy checkpoint. Rather, certain standard synchronization treatments cause damage that is the likely cause of G1 arrest. Since tetraploid cells can cycle when created with minimal manipulation, previous reports of a tetraploidy checkpoint can probably be explained by side effects of the drug treatments used to observe them.
Medicinal herb use among asthmatic patients attending a specialty care facility in Trinidad
Authors: Clement Yuri N , Williams Arlene F , Aranda Derick , Chase Ronald , Watson Nadya , Mohammed Rochelle , Stubbs Odia , Williamson Deneil 
Published: February 2005

Abstract
Background
There is an increasing prevalence of asthma in the Caribbean and patients remain non-compliant to therapy despite the development of guidelines for management and prevention. Some patients may self-medicate with medicinal herbs for symptomatic relief, as there is a long tradition of use for a variety of ailments. The study assessed the prevalence of use and the factors affecting the decision to use herbs in asthmatic patients attending a public specialty care clinic in Trinidad.

Methods
A descriptive, cross-sectional study was conducted at the Chest Clinic in Trinidad using a de novo, pilot-tested, researcher-administered questionnaire between June and July 2003.

Results
Fifty-eight out of 191 patients (30.4%) reported using herbal remedies for symptomatic relief. Gender, age, ethnicity, and asthma severity did not influence the decision to use herbs; however, 62.5% of patients with tertiary level schooling used herbs, p = 0.025. Thirty-four of these 58 patients (58.6%) obtained herbs from their backyards or the supermarket; only 14 patients (24.1%) obtained herbs from an herbalist, herbal shop or pharmacy. Relatives and friends were the sole source of information for most patients (70.7%), and only 10.3% consulted an herbalist. Ginger, garlic, aloes, shandileer, wild onion, pepper and black sage were the most commonly used herbs.

Conclusions
Among patients attending the Chest Clinic in Trinidad the use of herbal remedies in asthma is relatively common on the advice of relatives and friends. It is therefore becoming imperative for healthcare providers to become more knowledgeable on this modality and to keep abreast with the latest developments.