bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human β-Defensin 3 Inhibits Cell Wall Biosynthesis in Staphylococci
Authors: Sass Vera , Schneider Tanja , Wilmes Miriam , Körner Christian , Tossi Alessandro , Novikova Natalia , Shamova Olga , Sahl Hans-Georg 
Published: April 2010

ABSTRACTHuman β-defensin 3 (hBD3) is a highly charged (+11) cationic host defense peptide, produced by epithelial cells and neutrophils. hBD3 retains antimicrobial activity against a broad range of pathogens, including multiresistantStaphylococcus aureus, even under high-salt conditions. Whereas antimicrobial host defense peptides are assumed to act by permeabilizing cell membranes, the transcriptional response pattern of hBD3-treated staphylococcal cells resembled that of vancomycin-treated cells (V. Sass, U. Pag, A. Tossi, G. Bierbaum, and H. G. Sahl, Int. J. Med. Microbiol. 298:619-633, 2008) and suggested that inhibition of cell wall biosynthesis is a major component of the killing process. hBD3-treated cells, inspected by transmission electron microscopy, showed localized protrusions of cytoplasmic contents, and analysis of the intracellular pool of nucleotide-activated cell wall precursors demonstrated accumulation of the final soluble precursor, UDP-MurNAc-pentapeptide. Accumulation is typically induced by antibiotics that inhibit membrane-bound steps of cell wall biosynthesis and also demonstrates that hBD3 does not impair the biosynthetic capacity of cells and does not cause gross leakage of small cytoplasmic compounds. Inin vitroassays of individual membrane-associated cell wall biosynthesis reactions (MraY, MurG, FemX, and penicillin-binding protein 2 [PBP2]), hBD3 inhibited those enzymes which use the bactoprenol-bound cell wall building block lipid II as a substrate; quantitative analysis suggested that hBD3 may stoichiometrically bind to lipid II. We report that binding of hBD3 to defined, lipid II-rich sites of cell wall biosynthesis may lead to perturbation of the biosynthesis machinery, resulting in localized lesions in the cell wall as demonstrated by electron microscopy. The lesions may then allow for osmotic rupture of cells when defensins are tested under low-salt conditions.
Functional Significance of the E Loop, a Novel Motif Conserved in the Lantibiotic Immunity ATP-Binding Cassette Transport Systems
Authors: Okuda Ken-ichi , Yanagihara Sae , Sugayama Tomomichi , Zendo Takeshi , Nakayama Jiro , Sonomoto Kenji 
Published: April 2010

ABSTRACT
Lantibiotics are peptide-derived antibacterial substances produced by some Gram-positive bacteria and characterized by the presence of unusual amino acids, like lanthionines and dehydrated amino acids. Because lantibiotic producers may be attacked by self-produced lantibiotics, they express immunity proteins on the cytoplasmic membrane. An ATP-binding cassette (ABC) transport system mediated by the LanFEG protein complex is a major system in lantibiotic immunity. Multiple-sequence alignment analysis revealed that LanF proteins contain the E loop, a variant of the Q loop, which is a well-conserved motif in the nucleotide-binding domains (NBDs) of general ABC transporters. To elucidate E loop function, we introduced a mutation in the NukF protein, which is involved in the nukacin-ISK-1 immunity system. Amino acid replacement of glutamic acid in the E loop with glutamine (E85Q) resulted in slight decreases in the immunity level and transport activity. Additionally, the E85A mutation severely impaired the immunity level and transport activity. On the other hand, ATPase activities of purified E85Q and E85A mutants were almost similar to that of the wild type. These results suggested that the E loop found in ABC transporters involved in lantibiotic immunity plays a significant role in the function of these transporters, especially in the structural change of transmembrane domains.
RmpA Regulation of Capsular Polysaccharide Biosynthesis inKlebsiella pneumoniaeCG43
Authors: Cheng H. Y. , Chen Y. S. , Wu C. Y. , Chang H. Y. , Lai Y. C. , Peng H. L. 
Published: April 2010

ABSTRACTSequence analysis of the large virulence plasmid pLVPK inKlebsiella pneumoniaeCG43 revealed the presence of another mucoid factor encoding genermpAbesidesrmpA2. Promoter activity measurement indicated that the deletion ofrmpAreduced K2 capsular polysaccharide (CPS) biosynthesis, resulting in decreased colony mucoidy and virulence in mice. Introduction of a multicopy plasmid carryingrmpArestored CPS production in thermpAorrmpA2mutant but not in thercsBmutant. Transformation of thermpAdeletion mutant with anrcsB-carrying plasmid also failed to enhance CPS production, suggesting that a cooperation of RmpA with RcsB is required for regulatory activity. This was further corroborated by the demonstration ofin vivointeraction between RmpA and RcsB using two-hybrid analysis and coimmunoprecipitation analysis. A putative Fur binding box was only found at the 5′ noncoding region ofrmpA. The promoter activity analysis indicated that the deletion offurincreased thermpApromoter activity. Using electrophoretic mobility shift assay, we further demonstrated that Fur exerts its regulatory activity by binding directly to the promoter. As a result, thefurdeletion mutant exhibited an increase in colony mucoidy, CPS production, and virulence in mice. In summary, our results suggested that RmpA activates CPS biosynthesis inK. pneumoniaeCG43 via an RcsB-dependent manner. The expression ofrmpAis regulated by the availability of iron and is negatively controlled by Fur.
PdhS, an Old-Pole-Localized Histidine Kinase, Recruits the Fumarase FumC in
Brucella abortus
Authors: Mignolet Johann , Van der Henst Charles , Nicolas Cécile , Deghelt Michaël , Dotreppe Delphine , Letesson Jean-Jacques , De Bolle Xavier 
Published: April 2010

ABSTRACT

The bacterial pathogen
Brucella abortus
was recently demonstrated to recruit the essential cytoplasmic histidine kinase PdhS to its old pole. Here, we report identification of the fumarase FumC as a specific partner for the N-terminal “sensing” domain of PdhS, using an ORFeome-based yeast two-hybrid screen. We observed that FumC and PdhS colocalize at the old pole of
B. abortus
, while the other fumarase FumA is not polarly localized. FumC is not required for PdhS localization, and polar FumC localization is not FumA dependent. FumC homologs are not polarly localized in
Sinorhizobium meliloti
and
Caulobacter crescentus
, suggesting that polar recruitment of FumC by PdhS is evolutionarily recent.
Self-Assembly of the Bacterial Cytoskeleton-Associated RNA Helicase B Protein into Polymeric Filamentous Structures
Authors: Taghbalout Aziz , Yang Qingfen 
Published: April 2010

ABSTRACTTheEscherichia coliRNA degradosome proteins are organized into a helical cytoskeletal-like structure within the cell. Here we describe the ATP-dependent assembly of the RhlB component of the degradosome into polymeric filamentous structuresin vitro, which suggests that extended polymers of RhlB are likely to comprise a basic core element of the degradosome cytoskeletal structures.
SpoIID-Mediated Peptidoglycan Degradation Is Required throughout Engulfment during
Bacillus subtilis
Sporulation
Authors: Gutierrez Jennifer , Smith Rachelle , Pogliano Kit 
Published: April 2010

ABSTRACT

SpoIID is a membrane-anchored enzyme that degrades peptidoglycan and is essential for engulfment and sporulation in
Bacillus subtilis
. SpoIID is targeted to the sporulation septum, where it interacts with two other proteins required for engulfment: SpoIIP and SpoIIM. We changed conserved amino acids in SpoIID to alanine to determine whether there was a correlation between the effect of each substitution on the
in vivo
and
in vitro
activities of SpoIID. We identified one amino acid substitution, E88A, that eliminated peptidoglycan degradation activity and one, D210A, that reduced it, as well as two substitutions that destabilized the protein in
B. subtilis
(R106A and K203A). Using these mutants, we show that the peptidoglycan degradation activity of SpoIID is required for the first step of engulfment (septal thinning), as well as throughout membrane migration, and we show that SpoIID levels are substantially above the minimum required for engulfment. The inactive mutant E88A shows increased septal localization compared to the wild type, suggesting that the degradation cycle of the SpoIID/SpoIIP complex is accompanied by the activity-dependent release of SpoIID from the complex and subsequent rebinding. This mutant is also capable of moving SpoIIP across the sporulation septum, suggesting that SpoIID binding, but not peptidoglycan degradation activity, is needed for relocalization of SpoIIP. Finally, the mutant with reduced activity (D210A) causes uneven engulfment and time-lapse microscopy indicates that the fastest-moving membrane arm has greater concentrations of SpoIIP than the slower-moving arm, demonstrating a correlation between SpoIIP protein levels and the rate of membrane migration.
Complete Genome Sequence of “
Candidatus
Puniceispirillum marinum” IMCC1322, a Representative of the SAR116 Clade in the
Alphaproteobacteria
Authors: Oh Hyun-Myung , Kwon Kae Kyoung , Kang Ilnam , Kang Sung Gyun , Lee Jung-Hyun , Kim Sang-Jin , Cho Jang-Cheon 
Published: April 2010

ABSTRACT

The complete genome sequence of “
Candidatus
Puniceispirillum marinum” IMCC1322, the first cultured representative of the SAR116 clade in the
Alphaproteobacteria
, is reported here. The genome contains genes for proteorhodopsin, aerobic-type carbon monoxide dehydrogenase, dimethylsulfoniopropionate demethylase, and C
1
compound metabolism. The genome information proposes the SAR116 group to be metabolic generalists in ocean nutrient cycling.
Role of the FeoB Protein and Siderophore in Promoting Virulence ofXanthomonas oryzaepv. oryzae on Rice
Authors: Pandey Alok , Sonti Ramesh V. 
Published: April 2010

ABSTRACTXanthomonas oryzaepv. oryzae causes bacterial blight, a serious disease of rice. Our analysis revealed that theX. oryzaepv. oryzae genome encodes genes responsible for iron uptake through FeoB (homolog of the major bacterial ferrous iron transporter) and a siderophore. A mutation in theX. oryzaepv. oryzaefeoBgene causes severe virulence deficiency, growth deficiency in iron-limiting medium, and constitutive production of a siderophore. We identified an iron regulatedxssgene cluster, in whichxssABCDE(Xanthomonassiderophoresynthesis) andxsuA(Xanthomonassiderophoreutilization) genes encode proteins involved in biosynthesis and utilization ofX. oryzaepv. oryzae siderophore. Mutations in thexssA,xssB, andxssEgenes cause siderophore deficiency and growth restriction under iron-limiting conditions but are virulence proficient. AnxsuAmutant displayed impairment in utilization of native siderophore, suggesting that XsuA acts as a specific receptor for a ferric-siderophore complex. Histochemical and fluorimetric assays withgusAfusions indicate that, duringin plantagrowth, thefeoBgene is expressed and that thexssoperon is not expressed. This study represents the first report describing a role forfeoBin virulence of any plant-pathogenic bacterium and the first functional characterization of a siderophore-biosynthetic gene cluster in any xanthomonad.
Down regulation of prothrombinase by activated protein C during prothrombin activation
Authors: Y. Kim Paul , E. Nesheim Michael 
Published: April 2010

SummaryActivated protein C (aPC) proteolytically inactivates factor Va (FVa) and thereby downregulates prothrombinase. Although FVa inactivation by aPC has been studied extensively, the inactivation of prothrombinase during prothrombin activation has not. Therefore, prothrombin activation initiated both without and with aPC (5.0, 7.5 or 10.0 nM) was monitored over time by fluorescence. The experiments were performed with 0.075 nM FVa and 1.0 nM FXa, and with these concentrations reversed. The time courses of the residual prothrombinase activity with aPC, determined from the slopes of fluorescence over time, were pseudo first order with both limiting and excess FVa. With FVa limiting or in excess, the second rate constants for inactivation of prothrombinase were 1.98 ± 0.09 x 105 M-1s-1 and 2.54 ± 0.13 x 105 M-1s-1 , respectively. The former value is 101-fold smaller than that for FVa inactivation by aPC alone. Since with limiting FVa the second order rate constants for prothrombinsase inactivation and FVa inactivation are equal, FVa is protected 101-fold, presumably by both FXa and prothrombin. In contrast, with excess FVa, the calculated rate constant for FVa inactivation exceeds that for prothrombinase inactivation 17.3-fold, which reflects a loss of protection by FXa. Since the protective effects of the two proteins are theoretically multiplicative, FXa protected 17.3-fold and prothrombin protected 5.8-fold. With 150 nM protein S and limiting FVa, prothrombinase inactivation was two-fold faster, yet it was still protected 91-fold. These studies show that FVa is down-regulated by aPC during prothrombin activation, but both FXa and prothrombin protect FVa in a multiplicative way, with or without protein S.
Determination of a factor VIII-interactive region within plasmin responsible for plasmin-catalysed activation and inactivation of factor VIII(a)
Authors: Nishiya Katsumi , Okada Kiyotaka , Matsuo Osamu , Takeyama Masahiro , Ogiwara Kenichi , Shima Midori , Nogami Keiji 
Published: April 2010

SummaryPlasmin, an active form of plasminogen, activates and inactivates factor VIII (FVIII) by limited proteolysis. We have previously identifiedly sine-binding site-independent plasmin-interactive sites on the FVIII A2 domain responsible for cleavages at Arg336 and Arg372, together with lysine-binding site-dependent plasmin sites on the light chain responsible for cleavage at Lys36. We have now characterised FVIII-interactive regions on plasmin. SDS-PAGE analysis demonstrated that a monoclon al antibody (mAb) against kringle (K)5-catalytic domain (K5-CD) of plasmin significantly blocked plasmin-catalysed cleavages at Arg336 and Arg372. K5-CD fragment and this mAb blocked plasmincatalysed activation and inactivation of FVIII(a). Anti-K1–2–3 and anti-K4 mAbs blocked plasmin-catalysed cleavages at Lys36, and K1–2–3 and K4 fragments inhibited plasmin-catalysed inactivation of A11–336 FVIIIa. The K5-CD preferentially bound to the A2 domain (Kd app ; 52 nM), whilst the K1–2–3 and K4 bound to the light chain (Kd app; 75 and 106 nM, respectively) in ELISA. Binding was attributed to the A2 484–509 region and A3 1690–1705/1804–1818 region, respectively. 6-aminohexanoic acid, a lysine analogue, significantly inhibited the light chain/K1–2–3 (and K4) binding by ∼90%, whilst A2/K5-CD binding was moderated by only ∼35%. Furthermore, an anti-CD antibody blocked plasmin-catalysed cleavage by inhibiting the A2/K5-CD interaction. These data demon strate that the K5-CD of plasmin (and plasminogen) interacts with the A2 domain independent of lysine-binding site, whilst interactions of K1–2–3 and K4 with the light chain are lysine-binding site-dependent. Interactions between the K5-CD and A2 likely constitute the major regulatory mechanism for activation and inactivation of FVIII(a) mediated by cleavage at Arg372 and Arg336.
Angiopoietin-2 plasma dosage predicts time to first treatment and overall survival in chronic lymphocytic leukemia
Authors: Maffei Rossana , Martinelli Silvia , Santachiara Rita , Rossi Davide , Guarnotta Carla , Sozzi Elisa , Zucchetto Antonella , Rigolin Gian Matteo , Fiorcari Stefania , Castelli Ilaria , Fontana Marcella , Coluccio Valeria , Leonardi Giovanna , Zucchini Patrizia , Tripodo Claudio , Cuneo Antonio , Gattei Valter , Del Poeta Giovanni , Forconi Francesco , Gaidano Gianluca , Torelli Giuseppe , Marasca Roberto 
Published: April 2010

AbstractThe clinical relevance of angiopoietin-2 (Ang2) in chronic lymphocytic leukemia (CLL) was previously suggested by the association between high Ang2, and shorter progression-free survival reported in small series of patients. Here, we evaluated Ang2 glycoprotein levels in plasma samples collected from a multicentric cohort of CLL patients (n = 316) using an enzyme-linked immunosorbent assay method, and we investigated its prognostic role in relation to time to first treatment (TTFT) and overall survival. Based on a cutoff equal to 2459 pg/mL, we divided our cohort in 2 subsets (high and low Ang2) composing 100 (31.6%) and 216 (68.4%) patients, respectively. High Ang2 was predictive of reduced TTFT (P < .001) and overall survival (P = .002). Multivariate analysis confirmed that high Ang2 was an independent prognosticator for TTFT (hazard ratio = 1.739; 95% confidence interval, 1.059-2.857; P = .029). Significant associations were found between high Ang2 and advanced Binet stages (P < .001), high β2-microglobulin (P < .001), unmutated variable region of immunoglobulin heavy chain gene status (P < .001), high CD38 and ζ-chain-associated protein kinase 70 expression (P < .001 and P = .003), and intermediate/high cytogenetic risk (P = .005). Moreover, Ang2 added prognostic power to other conventional prognosticators and helped to refine prognosis among CLL subsets with both high and low vascular endothelial growth factor plasma levels. Ang2 plasma level may be a useful independent prognosticator for CLL.
Adenosine A2A receptor agonists and PDE inhibitors: a synergistic multitarget mechanism discovered through systematic combination screening in B-cell malignancies
Authors: Rickles Richard J. , Pierce Laura T. , Giordano Thomas P. , Tam Winnie F. , McMillin Douglas W. , Delmore Jake , Laubach Jacob P. , Borisy Alexis A. , Richardson Paul G. , Lee Margaret S. 
Published: April 2010

Abstract
Using a combination high-throughput screening technology, multiple classes of drugs and targeted agents were identified that synergize with dexamethasone (Dex) in multiple myeloma (MM) cells. Performing combination screening with these enhancers, we discovered an unexpected synergistic interaction between adenosine receptor agonists and phosphodiesterase (PDE) inhibitors that displays substantial activity in a panel of MM and diffuse large B-cell lymphoma (DLBCL) cell lines and tumor cells from MM patients. We have used selective adenosine receptor agonists, antagonists, and PDE inhibitors as well as small interfering RNAs targeting specific molecular isoforms of these proteins to dissect the molecular mechanism of this synergy. The adenosine A2A receptor and PDE2, 3, 4, and 7 are important for activity. Drug combinations induce cyclic AMP (cAMP) accumulation and up-regulate PDE4B. We also observe rigorous mathematical synergy in 3-way combinations containing A2A agonists, PDE inhibitors, and Dex at multiple concentrations and ratios. Taken together, these data suggest that A2A agonist/PDE inhibitor combinations may be attractive as an adjunctive to clinical glucocorticoid containing regiments for patients with MM or DLBCL and confer benefit in both glucocorticoid-sensitive and -resistant populations.
Bacteria in cancer therapy: a novel experimental strategy
Authors: Patyar S , Joshi R , Byrav DS Prasad , Prakash A , Medhi B , Das BK 
Published: April 2010

AbstractResistance to conventional anticancer therapies in patients with advanced solid tumors has prompted the need of alternative cancer therapies. Moreover, the success of novel cancer therapies depends on their selectivity for cancer cells with limited toxicity to normal tissues. Several decades after Coley's work a variety of natural and genetically modified non-pathogenic bacterial species are being explored as potential antitumor agents, either to provide direct tumoricidal effects or to deliver tumoricidal molecules. Live, attenuated or genetically modified non-pathogenic bacterial species are capable of multiplying selectively in tumors and inhibiting their growth. Due to their selectivity for tumor tissues, these bacteria and their spores also serve as ideal vectors for delivering therapeutic proteins to tumors. Bacterial toxins too have emerged as promising cancer treatment strategy. The most potential and promising strategy is bacteria based gene-directed enzyme prodrug therapy. Although it has shown successful resultsin vivoyet further investigation about the targeting mechanisms of the bacteria are required to make it a complete therapeutic approach in cancer treatment.
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study
Authors: Liu Qi , Xu Qian , Zheng Vincent W , Xue Hong , Cao Zhiwei , Yang Qiang 
Published: April 2010

Abstract

Background
Gene silencing using exogenous small interfering RNAs (siRNAs) is now a widespread molecular tool for gene functional study and new-drug target identification. The key mechanism in this technique is to design efficient siRNAs that incorporated into the RNA-induced silencing complexes (RISC) to bind and interact with the mRNA targets to repress their translations to proteins. Although considerable progress has been made in the computational analysis of siRNA binding efficacy, few joint analysis of different RNAi experiments conducted under different experimental scenarios has been done in research so far, while the joint analysis is an important issue in cross-platform siRNA efficacy prediction. A collective analysis of RNAi mechanisms for different datasets and experimental conditions can often provide new clues on the design of potent siRNAs.

Results
An elegant multi-task learning paradigm for cross-platform siRNA efficacy prediction is proposed. Experimental studies were performed on a large dataset of siRNA sequences which encompass several RNAi experiments recently conducted by different research groups. By using our multi-task learning method, the synergy among different experiments is exploited and an efficient multi-task predictor for siRNA efficacy prediction is obtained. The 19 most popular biological features for siRNA according to their jointly importance in multi-task learning were ranked. Furthermore, the hypothesis is validated out that the siRNA binding efficacy on different messenger RNAs(mRNAs) have different conditional distribution, thus the multi-task learning can be conducted by viewing tasks at an "mRNA"-level rather than at the "experiment"-level. Such distribution diversity derived from siRNAs bound to different mRNAs help indicate that the properties of target mRNA have important implications on the siRNA binding efficacy.

Conclusions
The knowledge gained from our study provides useful insights on how to analyze various cross-platform RNAi data for uncovering of their complex mechanism.