bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Phenylpyruvate Decarboxylase, Involved in Auxin Production of
Azospirillum brasilense
Authors: Spaepen Stijn , Versées Wim , Gocke Dörte , Pohl Martina , Steyaert Jan , Vanderleyden Jos 
Published: September 2007

ABSTRACT

Azospirillum brasilense
belongs to the plant growth-promoting rhizobacteria with direct growth promotion through the production of the phytohormone indole-3-acetic acid (IAA). A key gene in the production of IAA, annotated as indole-3-pyruvate decarboxylase (
ipdC
), has been isolated from
A. brasilense
, and its regulation was reported previously (A. Vande Broek, P. Gysegom, O. Ona, N. Hendrickx, E. Prinsen, J. Van Impe, and J. Vanderleyden, Mol. Plant-Microbe Interact. 18:311-323, 2005). An
ipdC
-knockout mutant was found to produce only 10% (wt/vol) of the wild-type IAA production level. In this study, the encoded enzyme is characterized via a biochemical and phylogenetic analysis. Therefore, the recombinant enzyme was expressed and purified via heterologous overexpression in
Escherichia coli
and subsequent affinity chromatography. The molecular mass of the holoenzyme was determined by size-exclusion chromatography, suggesting a tetrameric structure, which is typical for 2-keto acid decarboxylases. The enzyme shows the highest
k
cat
value for phenylpyruvate. Comparing values for the specificity constant
k
cat
/

K
m

, indole-3-pyruvate is converted 10-fold less efficiently, while no activity could be detected with benzoylformate. The enzyme shows pronounced substrate activation with indole-3-pyruvate and some other aromatic substrates, while for phenylpyruvate it appears to obey classical Michaelis-Menten kinetics. Based on these data, we propose a reclassification of the
ipdC
gene product of
A. brasilense
as a phenylpyruvate decarboxylase (EC 4.1.1.43).
Genetic Relatedness of theStreptococcus pneumoniaeCapsular Biosynthetic Loci
Authors: Mavroidi Angeliki , Aanensen David M. , Godoy Daniel , Skovsted Ian C. , Kaltoft Margit S. , Reeves Peter R. , Bentley Stephen D. , Spratt Brian G. 
Published: September 2007

ABSTRACTStreptococcus pneumoniae(the pneumococcus) produces 1 of 91 capsular polysaccharides (CPS) that define the serotype. Thecpsloci of 88 pneumococcal serotypes whose CPS is synthesized by the Wzy-dependent pathway were compared with each other and with additional streptococcal polysaccharide biosynthetic loci and were clustered according to the proportion of shared homology groups (HGs), weighted for the sequence similarities between the genes encoding the shared HGs. Thecpsloci of the 88 pneumococcal serotypes were distributed into eight major clusters and 21 subclusters. All serotypes within the same serogroup fell into the same major cluster, but in six cases, serotypes within the same serogroup were in different subclusters and, conversely, nine subclusters included completely different serotypes. The closely relatedcpsloci within a subcluster were compared to the known CPS structures to relate gene content to structure. TheStreptococcus oralisandStreptococcus mitispolysaccharide biosynthetic loci clustered within the pneumococcalcpsloci and were in a subcluster that also included thecpslocus of pneumococcal serotype 21, whereas theStreptococcus agalactiae cpsloci formed a single cluster that was not closely related to any of the pneumococcalcpsclusters.
Predicted Functions and Linkage Specificities of the Products of theStreptococcus pneumoniaeCapsular Biosynthetic Loci
Authors: Aanensen David M. , Mavroidi Angeliki , Bentley Stephen D. , Reeves Peter R. , Spratt Brian G. 
Published: September 2007

ABSTRACTThe sequences of the capsular biosynthetic (cps) loci of 90 serotypes ofStreptococcus pneumoniaehave recently been determined. Bioinformatic procedures were used to predict the general functions of 1,973 of the 1,999 gene products and to identify proteins within the same homology group, Pfam family, and CAZy glycosyltransferase family. Correlatingcpsgene content with the 54 known capsular polysaccharide (CPS) structures provided tentative assignments of the specific functions of the different homology groups of each functional class (regulatory proteins, enzymes for synthesis of CPS constituents, polymerases, flippases, initial sugar transferases, glycosyltransferases [GTs], phosphotransferases, acetyltransferases, and pyruvyltransferases). Assignment of the glycosidic linkages catalyzed by the 342 GTs (92 homology groups) is problematic, but tentative assignments could be made by using this large set ofcpsloci and CPS structures to correlate the presence of particular GTs with specific glycosidic linkages, by correlating inverting or retaining linkages in CPS repeat units with the inverting or retaining mechanisms of the GTs predicted from their CAZy family membership, and by comparing the CPS structures of serotypes that have very similarcpsgene contents. These large-scale comparisons between structure and gene content assigned the linkages catalyzed by 72% of the GTs, and all linkages were assigned in 32 of the serotypes with known repeat unit structures. Clear examples where very similar initial sugar transferases or glycosyltransferases catalyze different linkages in different serotypes were also identified. These assignments should provide a stimulus for biochemical studies to evaluate the reactions that are proposed.
Identification of Novel Surface Proteins ofAnaplasma phagocytophilumby Affinity Purification and Proteomics
Authors: Ge Yan , Rikihisa Yasuko 
Published: September 2007

ABSTRACTAnaplasma phagocytophilumis the etiologic agent of human granulocytic anaplasmosis (HGA), one of the major tick-borne zoonoses in the United States. The surface ofA. phagocytophilumplays a crucial role in subverting the hostile host cell environment. However, except for the P44/Msp2 outer membrane protein family, the surface components ofA. phagocytophilumare largely unknown. To identify the major surface proteins ofA. phagocytophilum, a membrane-impermeable, cleavable biotin reagent, sulfosuccinimidyl-2-[biotinamido]ethyl-1,3-dithiopropionate (Sulfo-NHS-SS-Biotin), was used to label intact bacteria. The biotinylated bacterial surface proteins were isolated by streptavidin agarose affinity purification and then separated by electrophoresis, followed by capillary liquid chromatography-nanospray tandem mass spectrometry analysis. Among the major proteins captured by affinity purification were fiveA. phagocytophilumproteins, Omp85, hypothetical proteins APH_0404 (designated Asp62) and APH_0405 (designated Asp55), P44 family proteins, and Omp-1A. The surface exposure of Asp62 and Asp55 was verified by immunofluorescence microscopy. Recombinant Asp62 and Asp55 proteins were recognized by an HGA patient serum. Anti-Asp62 and anti-Asp55 peptide sera partially neutralizedA. phagocytophiluminfection of HL-60 cells in vitro. We found that the Asp62 and Asp55 genes were cotranscribed and conserved among members of the familyAnaplasmataceae. With the exception of P44-18, all of the proteins were newly revealed major surface-exposed proteins whose study should facilitate understanding the interaction betweenA. phagocytophilumand the host. These proteins may serve as targets for development of chemotherapy, diagnostics, and vaccines.
Analysis of Promoter Targets forEscherichia coliTranscription Elongation Factor GreA In Vivo and In Vitro
Authors: Stepanova Ekaterina , Lee Jookyung , Ozerova Maria , Semenova Ekaterina , Datsenko Kirill , Wanner Barry L. , Severinov Konstantin , Borukhov Sergei 
Published: September 2007

ABSTRACTTranscription elongation factor GreA induces nucleolytic activity of bacterial RNA polymerase (RNAP). In vitro, transcript cleavage by GreA contributes to transcription efficiency by (i) suppressing pauses and arrests, (ii) stimulating RNAP promoter escape, and (iii) enhancing transcription fidelity. However, it is unclear which of these functions is (are) most relevant in vivo. By comparing global gene expression profiles ofEscherichia colistrains lacking Gre factors and strains expressing either the wild type (wt) or a functionally inactive GreA mutant, we identified genes that are potential targets of GreA action. Data analysis revealed that in the presence of chromosomally expressed GreA, 19 genes are upregulated; an additional 105 genes are activated upon overexpression of the wt but not the mutant GreA. Primer extension reactions with selected transcription units confirmed the gene array data. The most prominent stimulatory effect (threefold to about sixfold) of GreA was observed for genes of ribosomal protein operons and thetnaoperon, suggesting that transcript cleavage by GreA contributes to optimal expression levels of these genes in vivo. In vitro transcription assays indicated that the stimulatory effect of GreA upon the transcription of these genes is mostly due to increased RNAP recycling due to facilitated promoter escape. We propose that transcript cleavage during early stages of initiation is thus the main in vivo function of GreA. Surprisingly, the presence of the wt GreA also led to the decreased transcription of many genes. The mechanism of this effect is unknown and may be indirect.
RelA-Dependent (p)ppGpp Production Controls Exoenzyme Synthesis inErwinia carotovorasubsp.atroseptica
Authors: Wang Jinhong , Gardiol Noemie , Burr Tom , Salmond George P. C. , Welch Martin 
Published: September 2007

ABSTRACTIn this report, we investigate the link between nutrient limitation, RelA-mediated (p)ppGpp production, and virulence in the phytopathogenErwinia carotovorasubsp.atroseptica. ArelAnull mutant (JWC7) was constructed by allelic exchange, and we confirmed that, unlike the wild-type progenitor, this mutant did not produce elevated levels of (p)ppGpp upon nutrient downshift. However, (p)ppGpp production could be restored in strain JWC7 during nutrient limitation by supplyingrelAintrans. During growth on exoenzyme-inducing minimal medium, therelAmutant showed a diminution in secreted pectate lyase and protease activities and a severe defect in motility. TherelAmutant was also impaired in its ability to cause rot in potato tubers. In the presence of serine hydroxamate (a competitive inhibitor of seryl tRNA synthase and a potent inducer of the stringent response in wild-typeE. carotovorasubsp.atroseptica), exoenzyme production was essentially abolished in JWC7 but could be restored in the presence of plasmid-bornerelA. The inhibition of exoenzyme production in JWC7 caused by serine hydroxamate could not be overcome by addition of the quorum-sensing signal molecule,N-3-oxohexanoyl-l-homoserine lactone. Quantitative reverse transcription-PCR analysis of selected RNA species confirmed that the effects ofrelAon secreted pectate lyase activity and motility could be attributed to a reduction in transcription of the corresponding genes. We conclude that nutrient limitation is a potent environmental cue that triggers (p)ppGpp-dependent exoenzyme production inE. carotovorasubsp.atroseptica. Furthermore, our data suggest that nutrient limitation [or rather, (p)ppGpp accumulation] is a prerequisite for effective quorum-sensing-dependent activation of exoenzyme production.
Peptide Signals Encode Protein Localization
Authors: Russell Jay H. , Keiler Kenneth C. 
Published: September 2007

ABSTRACTMany bacterial proteins are localized to precise intracellular locations, but in most cases the mechanism for encoding localization information is not known. Screening libraries of peptides fused to green fluorescent protein identified sequences that directed the protein to helical structures or to midcell. These peptides indicate that protein localization can be encoded in 20-amino-acid peptides instead of complex protein-protein interactions and raise the possibility that the location of a protein within the cell could be predicted from bioinformatic data.
Proteins Associated with theMyxococcus xanthusExtracellular Matrix
Authors: Curtis Patrick D. , Atwood James , Orlando Ron , Shimkets Lawrence J. 
Published: September 2007

ABSTRACTFruiting body formation ofMyxococcus xanthus, like biofilm formation of many other organisms, involves the production of an extracellular matrix (ECM). While the polysaccharide component has been studied, the protein component has been largely unexplored. Proteins associated with the ECM were solubilized from purified ECM by boiling with sodium dodecyl sulfate and were identified by liquid chromatography-tandem mass spectrometry of tryptic fragments. The ECM is enriched in proteins of novel function; putative functions were assigned for only 5 of the 21 proteins. Thirteen putative ECM proteins had lipoprotein secretion signals. The genes for many ECM proteins were disrupted in the wild-type (WT),fibA, andpilAbackgrounds. Disruption of the MXAN4860 gene had no effect in the WT orfibAbackground but in thepilAbackground resulted in a 24-h delay in aggregation and sporulation compared to its parent. The results of this study show that theM. xanthusECM proteome is diverse and novel.
Effect of a Small, Acid-Soluble Spore Protein from
Clostridium perfringens
on the Resistance Properties of
Bacillus subtilis
Spores
Authors: Leyva-Illades Juan Francisco , Setlow Barbara , Sarker Mahfuzur R. , Setlow Peter 
Published: September 2007

ABSTRACT

α/β-type small, acid-soluble spore proteins (SASP) are essential for the resistance of DNA in spores of
Bacillus
species to damage. An α/β-type SASP, Ssp2, from
Clostridium perfringens
was expressed at significant levels in
B. subtilis
spores lacking one or both major α/β-type SASP (α
−
and α
−
β
−
strains, respectively). Ssp2 restored some of the resistance of α
−
β
−
spores to UV and nitrous acid and of α
−
spores to dry heat. Ssp2 also restored much of the resistance of α
−
spores to nitrous acid and restored full resistance of α
−
spores to UV and moist heat. These results further indicate the interchangeability of α/β-type SASP in DNA protection in spores.
The phosphatidylinositol 3-kinase inhibitor, PX-866, is a potent inhibitor of cancer cell motility and growth in three-dimensional cultures
Authors: Howes Amy L. , Chiang Gary G. , Lang Elizabeth S. , Ho Caroline B. , Powis Garth , Vuori Kristiina , Abraham Robert T. 
Published: September 2007

AbstractThe phosphatidylinositol 3-kinase (PI3K) pathway is activated in many human tumors and mediates processes such as cell proliferation, survival, adhesion, and motility. The natural product, wortmannin, has been widely used to study the functional consequences of PI3K inhibition in both normal and transformed cells in culture but is not a suitable cancer chemotherapeutic agent due to stability and toxicity issues. PX-866, an improved wortmannin analogue, displays significant antitumor activity in xenograft models. Here, we directly compare PX-866 and wortmannin in human cancer cell lines cultured in monolayer or as three-dimensional spheroids. Both PI3K inhibitors failed to inhibit monolayer cell growth at concentrations up to 100 nmol/L but strongly suppressed spheroid growth at low nanomolar concentrations, with PX-866 showing greater potency than wortmannin. Relative to wortmannin, PX-866 treatment results in a more sustained loss of Akt phosphorylation, suggesting that the increased potency of PX-866 is related to a more durable inhibition of PI3K signaling. PX-866 and wortmannin both inhibit spheroid growth without causing cytotoxicity, similar to known cytostatic agents, such as rapamycin. PX-866 also inhibits cancer cell motility at subnanomolar concentrations. These findings suggest that the antitumor activities of PX-866 stem from prolonged inhibition of the PI3K pathway and inhibition of cell motility. In addition, we propose that the use of three-dimensional tumor models is more predictive of in vivo growth inhibition by PI3K inhibitors in cancer cell lines lacking phosphatase and tensin homologue activity or expression. [Mol Cancer Ther 2007;6(9):2505–14]
A platelet biomarker for assessing phosphoinositide 3-kinase inhibition during cancer chemotherapy
Authors: Bowers Rita K. , Marder Philip , Green Lisa J. , Horn Candice L. , Faber Andrew L. , Thomas James E. 
Published: September 2007

Abstract
Thrombin cleavages of selective proteinase-activated receptors (PAR) as well as PAR-activating peptide ligands can initiate the phosphoinositide 3-kinase (PI3K) signaling cascade in platelets. Downstream to this event, fibrinogen receptors on platelets undergo conformational changes that enhance fibrinogen binding. In our study, we used this phenomenon as a surrogate biomarker for assessing effects on PI3K activity. Our method, using flow cytometric measurement of fluorescent ligand and antibody binding, uncovered a 16- to 45-fold signal window after PAR-induced platelet activation. Pretreatment (in vitro) with the PI3K inhibitors wortmannin and LY294002 resulted in concentration-dependent inhibition at predicted potencies. In addition, platelets taken from mice treated with wortmannin were blocked from PAR-induced ex vivo activation concomitantly with a decrease in phosphorylation of AKT from excised tumor xenografts. This surrogate biomarker assay was successfully tested (in vitro) on blood specimens received from volunteer cancer patients. Our results indicate that measurement of platelet activation could serve as an effective drug activity biomarker during clinical evaluation of putative PI3K inhibitors. [Mol Cancer Ther 2007;6(9):2600–7]
The combination of novel low molecular weight inhibitors of RAF (LBT613) and target of rapamycin (RAD001) decreases glioma proliferation and invasion
Authors: Hjelmeland Anita B. , Lattimore Kathryn P. , Fee Brian E. , Shi Qing , Wickman Sarah , Keir Stephen T. , Hjelmeland Mark D. , Batt David , Bigner Darell D. , Friedman Henry S. , Rich Jeremy N. 
Published: September 2007

Abstract
Monotherapies have proven largely ineffective for the treatment of glioblastomas, suggesting that increased patient benefit may be achieved by combining therapies. Two protumorigenic pathways known to be active in glioblastoma include RAS/RAF/mitogen-activated protein kinase and phosphatidylinositol 3-kinase/AKT/target of rapamycin (TOR). We investigated the efficacy of a combination of novel low molecular weight inhibitors LBT613 and RAD001 (everolimus), which were designed to target RAF and TOR, respectively. LBT613 decreased phosphorylation of extracellular signal-regulated kinase 1 and 2, downstream effectors of RAF, in a human glioma cell line. RAD001 resulted in decreased phosphorylation of the TOR effector S6. To determine if targeting RAF and TOR activities could result in decreased protumorigenic glioma cellular behaviors, we evaluated the abilities of LBT613 and RAD001 to affect the proliferation, migration, and invasion of human glioma cells. Treatment with either LBT613 or RAD001 alone significantly decreased the proliferation of multiple human glioma cell lines. Furthermore, LBT613 and RAD001 in combination synergized to decrease glioma cell proliferation in association with G1 cell cycle arrest. Glioma invasion is a critical contributor to tumor malignancy. The combination of LBT613 and RAD001 inhibited the invasion of human glioma cells through Matrigel to a greater degree than treatment with either drug alone. These data suggest that the combination of LBT613 and RAD001 reduces glioma cell proliferation and invasion and support examination of the combination of RAF and TOR inhibitors for the treatment of human glioblastoma patients. [Mol Cancer Ther 2007;6(9):2449–57]
Cutaneous castleman's disease responds to anti–interleukin-6 treatment
Authors: Ahmed Bilal , Tschen Jaime A. , Cohen Philip R. , Zaki Mohamed H. , Rady Peter L. , Tyring Stephen K. , Corringham Robert E. , Kurzrock Razelle 
Published: September 2007

AbstractCastleman's disease is uncommon, and cutaneous involvement is even rarer. We report a 42-year-old Asian woman with the multicentric plasma cell variant of Castleman's disease limited to her skin. The literature suggests that Castleman's disease is driven by interleukin-6 (IL-6). Based on these data, we hypothesized that suppression of IL-6 would have a salutary effect. Therefore, our patient was treated with CNTO328, a chimeric murine anti-human IL-6 antibody. She has shown a remarkable, ongoing response to this treatment, with almost complete clearing of her skin lesions after six doses. [Mol Cancer Ther 2007;6(9):2386–90]
BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features
Authors: Tsai Richard Tzong-Han , Chou Wen-Chi , Su Ying-Shan , Lin Yu-Chun , Sung Cheng-Lung , Dai Hong-Jie , Yeh Irene Tzu-Hsuan , Ku Wei , Sung Ting-Yi , Hsu Wen-Lian 
Published: September 2007

Abstract

Background
Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical field. A key IE task in this field is the extraction of biomedical relations, such as protein-protein and gene-disease interactions. However, most biomedical relation extraction systems usually ignore adverbial and prepositional phrases and words identifying location, manner, timing, and condition, which are essential for describing biomedical relations. Semantic role labeling (SRL) is a natural language processing technique that identifies the semantic roles of these words or phrases in sentences and expresses them as predicate-argument structures. We construct a biomedical SRL system called BIOSMILE that uses a maximum entropy (ME) machine-learning model to extract biomedical relations. BIOSMILE is trained on BioProp, our semi-automatic, annotated biomedical proposition bank. Currently, we are focusing on 30 biomedical verbs that are frequently used or considered important for describing molecular events.

Results
To evaluate the performance of BIOSMILE, we conducted two experiments to (1) compare the performance of SRL systems trained on newswire and biomedical corpora; and (2) examine the effects of using biomedical-specific features. The experimental results show that using BioProp improves the F-score of the SRL system by 21.45% over an SRL system that uses a newswire corpus. It is noteworthy that adding automatically generated template features improves the overall F-score by a further 0.52%. Specifically, ArgM-LOC, ArgM-MNR, and Arg2 achieve statistically significant performance improvements of 3.33%, 2.27%, and 1.44%, respectively.

Conclusion
We demonstrate the necessity of using a biomedical proposition bank for training SRL systems in the biomedical domain. Besides the different characteristics of biomedical and newswire sentences, factors such as cross-domain framesets and verb usage variations also influence the performance of SRL systems. For argument classification, we find that NE (named entity) features indicating if the target node matches with NEs are not effective, since NEs may match with a node of the parsing tree that does not have semantic role labels in the training set. We therefore incorporate templates composed of specific words, NE types, and POS tags into the SRL system. As a result, the classification accuracy for adjunct arguments, which is especially important for biomedical SRL, is improved significantly.