bluuebunny/crossref_metadata_2025_split huggingface dataset:
C68 from the Sulfolobus islandicus plasmid–virus pSSVx is a novel member of the AbrB-like transcription factor family
Authors: Contursi Patrizia , D'Ambrosio Katia , Pirone Luciano , Pedone Emilia , Aucelli Tiziana , She Qunxin , De Simone Giuseppina , Bartolucci Simonetta 
Published: February 2011

The genetic element pSSVx from Sulfolobus islandicus, strain REY15/4, is a hybrid between a plasmid and a fusellovirus. This plasmid–virus hybrid infects several species of the hyperthermophilic acidophilic crenarchaeon Sulfolobus. The open reading frame orfc68 of pSSVx encodes a 7.7 kDa protein that does not show significant sequence homology with any protein with known three-dimensional structure. EMSA (electrophoretic mobility-shift assay) experiments, DNA footprinting and CD analyses indicate that recombinant C68, purified from Escherichia coli, binds to two different operator sites that are located upstream of its own promoter. The three-dimensional structure, solved by a single-wavelength anomalous diffraction experiment on a selenomethionine derivative, shows that the protein assumes a swapped-hairpin fold, which is a distinctive fold associated with a family of prokaryotic transcription factors, such as AbrB from Bacillus subtilis. Nevertheless, C68 constitutes a novel representative of this family because it shows several peculiar structural and functional features.
Changes in cytosolic Mg2+ levels can regulate the activity of the plasma membrane H+-ATPase in maize
Authors: Hanstein Stefan , Wang Xiaozhi , Qian Xiaoqing , Friedhoff Peter , Fatima Ammara , Shan Yuhua , Feng Ke , Schubert Sven 
Published: February 2011

Plant PM (plasma membrane) H+-ATPase, a major consumer of cellular ATP, is driven by the MgATP complex which may dissociate at low cytosolic Mg2+ activity. We investigated whether hydrolytic activity of PM H+-ATPase is inhibited at ATP concentrations exceeding the Mg2+ concentration. Activity in isolated maize PMs was measured at pH 6.5 in the presence of 5 mM Mg2+ (high) or 2 mM Mg2+ (low), whereas K+ was applied at concentrations of 155 mM (high) or 55 mM (low). In all experiments, with membrane vesicles either from roots or leaves, the enzyme activity decreased in the presence of Mg2+-free ATP. At inhibitory ATP concentrations, the activity was not influenced by the K+ concentration. The activity was restored after increasing the Mg2+ concentration. ATP inhibition also occurred at pH 7.5. Kinetic modelling shows that Mg2+-free ATP acted as a competitive inhibitor with a Ki in the range of the Km. Ki decreased by 75% at low K+ concentration. Ki was one order of magnitude lower at pH 7.5 compared with pH 6.5. The observed inhibition is consistent with a concept in which down-regulation of the cytosolic Mg2+ activity is involved in (phyto)hormonal stress responses.
The role of TBK1 and IKKϵ in the expression and activation of Pellino 1
Authors: Smith Hilary , Liu Xin-Yu , Dai Liang , Goh Eddy T. H. , Chan Aye-Thu , Xi Jiajia , Seh Cheah-Chen , Qureshi Insaf A. , Lescar Julien , Ruedl Christiane , Gourlay Robert , Morton Simon , Hough Joanne , McIver Edward G. , Cohen Philip , Cheung Peter C. F. 
Published: February 2011

Mammalian Pellino isoforms are phosphorylated by IRAK (interleukin receptor associated kinase) 1/IRAK4 in vitro, converting them into active E3 ubiquitin ligases. In the present paper we report a striking enhancement in both transcription of the gene encoding Pellino 1 and Pellino 1 protein expression when murine BMDMs (bone-marrow-derived macrophages) are stimulated with LPS (lipopolysaccharide) or poly(I:C). This induction occurs via a TRIF [TIR (Toll/interleukin-1 receptor)-domain-containing adaptor-inducing interferon-β]-dependent IRAK-independent pathway and is prevented by inhibition of the IKK [IκB (inhibitor of nuclear factor κB) kinase]-related protein kinases, TBK1 {TANK [TRAF (tumour-necrosis-factor-receptor-associated factor)-associated nuclear factor κB activator]-binding kinase 1} and IKKϵ. Pellino 1 is not induced in IRF3 (interferon regulatory factor 3)−/− BMDMs, and its induction is only reduced slightly in type 1 interferon receptor−/− BMDMs, identifying Pellino 1 as a new IRF3-dependent gene. We also identify Pellino 1 in a two-hybrid screen using IKKϵ as bait, and show that IKKϵ/TBK1 activate Pellino 1 in vitro by phosphorylating Ser76, Thr288 and Ser293. Moreover, we show that the E3 ligase activity of endogenous Pellino 1 is activated in LPS- or poly(I:C)-stimulated macrophages. This occurs more rapidly than the increase in Pellino 1 mRNA and protein expression, is prevented by the inhibition of IKKϵ/TBK1 and is reversed by phosphatase treatment. Thus IKKϵ/TBK1 mediate the activation of Pellino 1's E3 ligase activity, as well as inducing the transcription of its gene and protein expression in response to TLR3 and TLR4 agonists.
Receptor-dependent compartmentalization of PPIP5K1, a kinase with a cryptic polyphosphoinositide binding domain
Authors: Gokhale Nikhil A. , Zaremba Angelika , Shears Stephen B. 
Published: February 2011

The inositol pyrophosphates are multifunctional signalling molecules. One of the families of enzymes that synthesize the inositol pyrophosphates are the Vip1/PPIP5Ks (PP-InsP5 kinases). The kinase domains in Vip1/PPIP5Ks have been mapped to their N-terminus. Each of these proteins also possess a phosphatase-like domain of unknown significance. In the present study, we show that this phosphatase-like domain is not catalytically active. Instead, by using SPR (surface plasmon resonance) to study protein binding to immobilized lipid vesicles, we show that this domain is specialized for binding PtdIns(3,4,5)P3 (PPIP5K1 Kd=96 nM; PPIP5K2 Kd=705 nM). Both PtdIns(3,4)P2 and PtdIns(4,5)P2 are significantly weaker ligands, and no significant binding of PtdIns(3,5)P2 was detected. We confirm the functional importance of this domain in inositol lipid binding by site-directed mutagenesis. We present evidence that the PtdIns(3,4,5)P3-binding domain is an unusual hybrid, in which a partial PH (pleckstrin homology) consensus sequence is spliced into the phosphatase-like domain. Agonist-dependent activation of the PtdIns 3-kinase pathway in NIH 3T3 cells drives translocation of PPIP5K1 from the cytosol to the plasma membrane. We have therefore demonstrated receptor-regulated compartmentalization of inositol pyrophosphate synthesis in mammalian cells.
Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue
Authors: Zhang Yong , Zhang Mengmeng , Zhang Yan 
Published: February 2011

Reversible phosphorylation of the CTD (C-terminal domain) of the eukaryotic RNA polymerase II largest subunit represents a critical regulatory mechanism during the transcription cycle and mRNA processing. Ssu72 is an essential phosphatase conserved in eukaryotes that dephosphorylates phosphorylated Ser5 of the CTD heptapeptide. Its function is implicated in transcription initiation, elongation and termination, as well as RNA processing. In the present paper we report the high resolution X-ray crystal structures of Drosophila melanogaster Ssu72 phosphatase in the apo form and in complex with an inhibitor mimicking the transition state of phosphoryl transfer. Ssu72 facilitates dephosphorylation of the substrate through a phosphoryl-enzyme intermediate, as visualized in the complex structure of Ssu72 with the oxo-anion compound inhibitor vanadate at a 2.35 Å (1 Å=0.1 nm) resolution. The structure resembles the transition state of the phosphoryl transfer with vanadate exhibiting a trigonal bi-pyramidal geometry covalently bonded to the nucleophilic cysteine residue. Interestingly, the incorporation of oxo-anion compounds greatly stabilizes a flexible loop containing the general acid, as detected by an increase of melting temperature of Ssu72 detected by differential scanning fluorimetry. The Ssu72 structure exhibits a core fold with a similar topology to that of LMWPTPs [low-molecular-mass PTPs (protein tyrosine phosphatases)], but with an insertion of a unique ‘cap’ domain to shelter the active site from the solvent with a deep groove in between where the CTD substrates bind. Mutagenesis studies in this groove established the functional roles of five residues (Met17, Pro46, Asp51, Tyr77 and Met85) that are essential specifically for substrate recognition.
How the biotin–streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer
Authors: Chivers Claire E. , Koner Apurba L. , Lowe Edward D. , Howarth Mark 
Published: February 2011

The interaction between SA (streptavidin) and biotin is one of the strongest non-covalent interactions in Nature. SA is a widely used tool and a paradigm for protein–ligand interactions. We previously developed a SA mutant, termed Tr (traptavidin), possessing a 10-fold lower off-rate for biotin, with increased mechanical and thermal stability. In the present study, we determined the crystal structures of apo-Tr and biotin–Tr at 1.5 Å resolution. In apo-SA the loop (L3/4), near biotin's valeryl tail, is typically disordered and open, but closes upon biotin binding. In contrast, L3/4 was shut in both apo-Tr and biotin–Tr. The reduced flexibility of L3/4 and decreased conformational change on biotin binding provide an explanation for Tr's reduced biotin off- and on-rates. L3/4 includes Ser45, which forms a hydrogen bond to biotin consistently in Tr, but erratically in SA. Reduced breakage of the biotin–Ser45 hydrogen bond in Tr is likely to inhibit the initiating event in biotin's dissociation pathway. We generated a Tr with a single biotin-binding site rather than four, which showed a simi-larly low off-rate, demonstrating that Tr's low off-rate was governed by intrasubunit effects. Understanding the structural features of this tenacious interaction may assist the design of even stronger affinity tags and inhibitors.
Peroxisomal multifunctional enzyme type 2 from the fruitfly: dehydrogenase and hydratase act as separate entities, as revealed by structure and kinetics
Authors: Haataja Tatu J. K. , Koski M. Kristian , Hiltunen J. Kalervo , Glumoff Tuomo 
Published: February 2011

All of the peroxisomal β-oxidation pathways characterized thus far house at least one MFE (multifunctional enzyme) catalysing two out of four reactions of the spiral. MFE type 2 proteins from various species display great variation in domain composition and predicted substrate preference. The gene CG3415 encodes for Drosophila melanogaster MFE-2 (DmMFE-2), complements the Saccharomyces cerevisiae MFE-2 deletion strain, and the recombinant protein displays both MFE-2 enzymatic activities in vitro. The resolved crystal structure is the first one for a full-length MFE-2 revealing the assembly of domains, and the data can also be transferred to structure–function studies for other MFE-2 proteins. The structure explains the necessity of dimerization. The lack of substrate channelling is proposed based on both the structural features, as well as by the fact that hydration and dehydrogenation activities of MFE-2, if produced as separate enzymes, are equally efficient in catalysis as the full-length MFE-2.
WT1 and its transcriptional cofactor BASP1 redirect the differentiation pathway of an established blood cell line
Authors: Goodfellow Sarah J. , Rebello Michelle R. , Toska Eneda , Zeef Leo A. H. , Rudd Sean G. , Medler Kathryn F. , Roberts Stefan G. E. 
Published: February 2011

The Wilms' tumour suppressor WT1 (Wilms' tumour 1) is a transcriptional regulator that plays a central role in organogenesis, and is mutated or aberrantly expressed in several childhood and adult malignancies. We previously identified BASP1 (brain acid-soluble protein 1) as a WT1 cofactor that suppresses the transcriptional activation function of WT1. In the present study we have analysed the dynamic between WT1 and BASP1 in the regulation of gene expression in myelogenous leukaemia K562 cells. Our findings reveal that BASP1 is a significant regulator of WT1 that is recruited to WT1-binding sites and suppresses WT1-mediated transcriptional activation at several WT1 target genes. We find that WT1 and BASP1 can divert the differentiation programme of K562 cells to a non-blood cell type following induction by the phorbol ester PMA. WT1 and BASP1 co-operate to induce the differentiation of K562 cells to a neuronal-like morphology that exhibits extensive arborization, and the expression of several genes involved in neurite outgrowth and synapse formation. Functional analysis revealed the relevance of the transcriptional reprogramming and morphological changes, in that the cells elicited a response to the neurotransmitter ATP. Taken together, the results of the present study reveal that WT1 and BASP1 can divert the lineage potential of an established blood cell line towards a cell with neuronal characteristics.
IQ-motif selectivity in human IQGAP2 and IQGAP3: binding of calmodulin and myosin essential light chain
Authors: Atcheson Erwan , Hamilton Elaine , Pathmanathan Sevvel , Greer Brett , Harriott Pat , Timson David J. 
Published: February 2011

The IQGAP [IQ-motif-containing GAP (GTPase-activating protein)] family members are eukaryotic proteins that act at the interface between cellular signalling and the cytoskeleton. As such they collect numerous inputs from a variety of signalling pathways. A key binding partner is the calcium-sensing protein CaM (calmodulin). This protein binds mainly through a series of IQ-motifs which are located towards the middle of the primary sequence of the IQGAPs. In some IQGAPs, these motifs also provide binding sites for CaM-like proteins such as myosin essential light chain and S100B. Using synthetic peptides and native gel electrophoresis, the binding properties of the IQ-motifs from human IQGAP2 and IQGAP3 have been mapped. The second and third IQ-motifs in IQGAP2 and all four of the IQ-motifs of IQGAP3 interacted with CaM in the presence of calcium ions. However, there were differences in the type of interaction: while some IQ-motifs were able to form complexes with CaM which were stable under the conditions of the experiment, others formed more transient interactions. The first IQ-motifs from IQGAP2 and IQGAP3 formed transient interactions with CaM in the absence of calcium and the first motif from IQGAP3 formed a transient interaction with the myosin essential light chain Mlc1sa. None of these IQ-motifs interacted with S100B. Molecular modelling suggested that all of the IQ-motifs, except the first one from IQGAP2 formed α-helices in solution. These results extend our knowledge of the selectivity of IQ-motifs for CaM and related proteins.
Impaired resistance artery function in patients with end-stage renal disease
Authors: Luksha Natallia , Luksha Leanid , Carrero Juan Jesús , Hammarqvist Folke , Stenvinkel Peter , Kublickiene Karolina 
Published: February 2011

We investigated an effect of uraemia on structural and functional features of human resistance vasculature. Arteries (≈ 200 μm) isolated from subcutaneous fat biopsies obtained from 35 ESRD (end-stage renal disease) patients starting peritoneal dialysis and 30 matched controls were studied using isolated small artery bioassays. Flow-mediated dilatation was attenuated in ESRD patients compared with controls. NO (nitric oxide) contribution to flow was lacking in ESRD patients, but present in the controls. ADMA (asymmetrical dimethyl L-arginine) levels were higher in the ESRD group compared with the control group. Dilatation in response to acetylcholine was reduced in ESRD patients compared with controls, but response to NO donor was similar. Expression of nitrotyrosine and heat shock proteins 70 and 27, but not 90, was increased in arteries from ESRD patients compared with controls. Arterial remodelling was absent in ESRD patients. There was no difference between the groups in myogenic tone, vascular reactivity or sensitivity to several vasoconstrictors. Arterial distensibility, reflecting passive properties of the vascular wall, was reduced in ESRD patients compared with controls. Exclusion of ESRD patients with diabetes and/or cardiovascular disease from analyses had no influence on the main findings. Thus we propose that uraemia has a strong impact on endothelial function and passive properties of the arterial wall of human peripheral resistance vasculature. The reduced contribution of NO to flow stimulus via enhanced nitrosative stress and higher plasma concentrations of ADMA may suggest potential mechanisms behind endothelial dysfunction in the resistance peripheral circulation in ESRD.
Identifying dispersed epigenomic domains from ChIP-Seq data
Authors: Song Qiang , Smith Andrew D. 
Published: February 2011

Abstract
Motivation: Post-translational modifications to histones have several well known associations with regulation of gene expression. While some modifications appear concentrated narrowly, covering promoters or enhancers, others are dispersed as epigenomic domains. These domains mark contiguous regions sharing an epigenomic property, such as actively transcribed or poised genes, or heterochromatically silenced regions. While high-throughput methods like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains, there remain important analysis problems that are not adequately solved by current analysis tools.
Results: We present the RSEG method for identifying epigenomic domains from ChIP-Seq data for histone modifications. In contrast with other methods emphasizing the locations of ‘peaks’ in read density profiles, our method identifies the boundaries of domains. RSEG is also able to incorporate a control sample and find genomic regions with differential histone modifications between two samples.
Availability: RSEG, including source code and documentation, is freely available at http://smithlab.cmb.usc.edu/histone/rseg/.
Contact: andrewds@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Intrahepatic Biliary Anomalies in a Patient With Mowat‐Wilson Syndrome Uncover a Role for the Zinc Finger Homeobox Gene zfhx1b in Vertebrate Biliary Development
Authors: Cui Shuang , Erlichman Jessi , Russo Pierre , Haber Barbara A , Matthews Randolph P 
Published: February 2011

ABSTRACTBackground:zfhz1b is the causative gene for Mowat‐Wilson syndrome, in which patients demonstrate developmental delay and Hirschsprung disease, as well as other anomalies.Materials and Methods:We identified a patient with Mowat‐Wilson syndrome who also developed cholestasis and histopathologic features consistent with biliary atresia, suggesting that mutations involving zfhz1b may lead to biliary developmental anomalies or injury to the biliary tract. We used the zebrafish model system to determine whether zfhx1b has a role in vertebrate biliary development.Results:Using zebrafish we determined that zfhx1b was expressed in the developing liver during biliary growth and remodeling, and that morpholino antisense oligonucleotide–mediated knockdown of zfhx1b led to defects in biliary development. These findings were associated with decreased expression of vhnf1, a transcription factor known to be important in biliary development in zebrafish and in mammals.Conclusions:Our studies underscore the importance of genetic contributions in the etiology of infantile hepatobiliary disorders, including biliary atresia.
Iron Load and Liver Enzymes in 10‐ and 13‐year‐olds
Authors: Okuda Masayuki , Sasaki Satoshi , Kunitsugu Ichiro , Sakurai Ryuta , Yoshitake Norikazu , Hobara Tatsuya 
Published: February 2011

ABSTRACTObjectives:Iron plays a pivotal role in adult steatosis, but its role in child and adolescent steatosis is unclear. We investigated the effect of dietary iron, serum iron, and ferritin on serum transaminases and γ‐glutamyltransferase in 10‐ and 13‐year‐olds.Patients and Methods:The study included 4894 fifth and eighth graders enrolled between 2006 and 2009 in all schools in Shunan City, Japan. Multiple regression analyses were performed with adjustments for grade, sex, z score of the body mass index, serum lipids, plasma glucose, frequency of sports activities, having a single parent, number of siblings, tobacco smoking behavior, passive smoking at home, resident areas, and schools, using linear mixed models. In addition, we analyzed ferritin and insulin resistance in randomly selected subset of participants.Results:Dietary iron intake was positively associated with serum alanine aminotransferase levels (standardized coefficient β = 2.35, P = 0.019). Serum iron concentrations were associated with transaminase and γ‐glutamyltransferase levels (β = 3.22, and 4.05, respectively, P < 0.01). In the subset of 421 subjects with further serum analysis, serum ferritin levels were significantly associated with serum enzyme levels (β = 2.43–3.35; P < 0.05) and showed significant odds ratio for the elevated alanine aminotransferase levels (1.05 for 1 SD with 95% confidence intervals 1.02–1.08). However, iron load did not show a positive association with insulin resistance.Conclusions:Although an effect size for iron is small in regression analyses, iron is implicated in increased transaminase levels in prepubertal and pubertal children.
Dietary Intake of Polyunsaturated Fatty Acids Among Breast‐feeding and Non–breast‐feeding 24‐ to 48‐month‐old Children in Bangladesh
Authors: Yakes Elizabeth A , Arsenault Joanne E , Islam M Munirul , Ahmed Tahmeed , German J Bruce , Drake Christiana , Hossain Mohammad B , Lewis Bess L , Rahman Ahmed Shafiqur , Jamil Kazi M , Brown Kenneth H 
Published: February 2011

ABSTRACTObjective:The aim of the study was to assess the adequacy of polyunsaturated fatty acid intake by rural Bangladeshi children 24 to 48 months old in relation to their breast‐feeding status.Materials and Methods:Multistage sampling was used to select a representative sample of children 24 to 48 months of age from 2 rural districts in Bangladesh (n = 479). Two nonconsecutive 24‐hour periods of dietary data were collected via 12‐hour daytime in‐home observations and recall. Breast milk intake was estimated using test weighing. The National Cancer Institute (NCI) method for episodically consumed foods was used to estimate distributions of usual food and nutrient intakes.Results:Based on the estimated intake distributions, >95% of the children had usual fat intakes <30% of total energy. Among 24‐ to 35‐month‐old (younger) and 36‐ to 48‐month‐old (older) children, respectively, 4% and 16% of breast‐feeding children and 31% and 41% of non–breast‐feeding children were estimated to consume <10% of total energy from fat. An estimated 80% of all of the children consumed <4% of total energy as linoleic acid, and 99% consumed <1% of energy as α‐linolenic acid. Younger breast‐feeding children had higher estimated average docosahexaenoic acid (DHA) intakes (0.04 g DHA/day) than their non–breast‐feeding counterparts (0.01 g DHA/day; P = 0.0005). Both breast‐feeding and non–breast‐feeding older children had estimated mean DHA intakes of 0.02 g/day (P = 0.74).Conclusions:Rural Bangladeshi children 24 to 48 months old, and especially those who have discontinued breast‐feeding, may benefit from increased fat consumption.