FEBS Letters - Articles in Press

A new hypothesis on the simultaneous direct and indirect proton pump mechanisms in NADH-quinone oxidoreductase (complex I) - Accepted Manuscript

Tomoko Ohnishi, Eiko Nakamaru-Ogiso, S. Tsuyoshi Ohnishi — 2010-09-02

Abstract: Recently, Sazanov’s group reported the X-ray structure of whole complex I [Nature, 465, 441 (2010)], which presented a strong clue for a “piston-like” structure as the key mechanism for the “indirect” proton pump. We have studied the NuoL subunit which has a high sequence similarity to Na+/H+ antiporters, as do the NuoM and N subunits. We constructed 27 site-directed NuoL mutants. Our data suggest that the H+/e− stoichiometry seems to have decreased from (4H+/2e−) in the wild-type to approximately (3H+/2e−) in NuoL mutants. We propose a revised hypothesis that each of the “direct” and the “indirect” proton pumps transports 2H+ per 2e−.

MicroRNA-24 targeting RNA-binding protein DND1 in tongue squamous cell carcinoma - Accepted Manuscript

2010-09-02

Abstract: Deregulations of microRNA have been frequently observed in tongue squamous cell carcinoma (TSCC), but their roles in tumorigenesis are not entirely clear. Here, we reported the up-regulation of miR-24 in TSCC. MiR-24 up-regulation reduced the expression of RNA-binding protein dead end 1 (DND1). Knockdown of miR-24 led to enhanced expression of DND1. The direct targeting of miR-24 to the DND1 mRNA was predicted bioinformatically and confirmed by luciferase reporter gene assays. Furthermore, the miR-24-mediated change in DND1 expression suppressed the expression of cyclin-dependent kinase inhibitor 1B (CDKN1B), and also led to enhanced proliferation and reduced apoptosis in TSCC cells.

Biochemical characterization of the RNA-hydrolytic activity of a pumpkin 2S albumin - Accepted Manuscript

Evandro Fei Fang, Jack Ho Wong, Peng Lin, Tzi Bun Ng — 2010-09-02

Abstract: A pumpkin 2S albumin with ribonuclease (RNase) activity was purified from pumpkin seeds (Cucurbita sp.) by liquid chromatographic techniques. It manifested potent RNase activity toward baker’s yeast RNA and calf liver RNA, and some polyhomoribonucleotides, including poly(A), poly(U) and poly(C) but not poly(G). Moreover, it was able to hydrolyze total RNA of both animal and plant origins. Ions such as Na+, Mg2+, Ca2+, and Zn2+ inhibited its RNase activity. Since RNase activity has not been previously reported in 2S albumins, this work may shed further light on the biological importance of this group of proteins.

Development of a cell-free system reveals an oxygen-labile step in the maturation of [NiFe]-hydrogenase 2 of Escherichia coli - Accepted Manuscript

2010-08-31

Abstract: By combining extracts from strains lacking genes encoding either the maturation enzymes or the large subunits of hydrogenases 1, 2 and 3 we could reconstitute in vitro under strictly anaerobic conditions 10-15% of the hydrogenase activity present in wild-type Escherichia coli extracts. Purified, unprocessed Strep-tagged variants of the hydrogenase 2 large subunit, HybC, isolated from either a ΔhybD (encoding the hydrogenase 2-specific protease) mutant or a strain deficient in HypF could also be matured to active, processed enzyme using this system. These studies reveal that minimally one step early on the hydrogenase maturation pathway is oxygen-labile.

Binding and catalysis of Humulus lupulus adenylate isopentenyltransferase for the synthesis of isopentenylated diadenosine polyphosphates - Accepted Manuscript

Hsing-Mao Chu, Feng-Yuan Chen, Tzu-Ping Ko, Andrew H.-J Wang — 2010-08-31

Abstract: Various plant developmental processes involve phytohormones such as cytokinins. Isopentenyltransferase (IPT) reaction is the key rate-limiting step in cytokinin biosynthesis that transfers the isopentenyl group from dimethylallyl diphosphate to the N6-amino group of adenine. Here, a series of diadenosine polyphosphates were screened as possible substrates of IPT, among which A(p)4A, A(p)5A and A(p)6A showed higher affinity than did the authentic substrates ADP and ATP. In addition, formation of mono-isopentenyl A(p)nA and di-isopentenyl A(p)nA was observed. Judging by the existing biosynthetic and hydrolytic systems for A(p)nA in plants, A(p)nA and isopentenyl-A(p)nA may occur in the plant cells, with functional importance.

Inverting character of family GH115 α-glucuronidases - Uncorrected Proof

Katarína Kolenová, Olena Ryabova, Mária Vršanská, Peter Biely — 2010-08-30

Abstract: α-Glucuronidases of glycoside hydrolase family 115 of the xylose-fermenting yeast Pichia stipitis and wood-destroying fungus Schizophyllum commune liberate 4-O-methyl-d-glucuronic acid residues from aldouronic acids and glucuronoxylan. The specific activities of both enzymes increased with polymerization degree of the acidic xylooligosaccharides and were inhibited by linear β-1,4-xylooligosaccharides. These results suggest interaction of the enzyme with several xylopyranosyl residues of the xylan main chain. Using 1H NMR spectroscopy and reduced aldopentaouronic acid (MeGlcA3Xyl4-ol) as a substrate, it was found that both enzymes are inverting glycoside hydrolases releasing 4-O-methyl-d-glucuronic acid (MeGlcA) as its β-anomer.

Modulation of interferon signaling by hepatitis C virus non-structural 5A protein: Implication of genotypic difference in interferon treatment - Corrected Proof

Sang-Min Kang, Seung-Jae Won, Gun-Hee Lee, Yun-Sook Lim, Soon B. Hwang — 2010-08-30

Abstract: Interferon (IFN) response rate in hepatitis C virus (HCV) patients has been varied with genotypes. In this study, we investigated the effects of HCV NS5A protein on IFN resistance and compared the genotypic differences of NS5A. We showed that IFN-α-, poly I:C-, and Sendai virus-induced ISRE transcriptional activities were inhibited by both genotype 1b and 2a NS5A protein. We demonstrated that not only genotype 1b but also genotype 2a NS5A exerted the similar extent of IFN-α-induced antiviral activity. We showed that NS5A derived from both genotype 1b and 2a showed no significant differential IFN responses as seen in HCV patients. These data imply that some other host factor may be involved in genotypic differences of IFN antagonism in HCV patients.

The density of extracellular matrix proteins regulates inflammation and insulin signaling in adipocytes - Corrected Proof

Qinkai Li, Akiko Hata, Chisato Kosugi, Nananko Kataoka, Makoto Funaki — 2010-08-30

Abstract: Cells can not only sense the type of extracellular matrix (ECM) protein that is present in the microenvironment, but they can also sense its density. Here, we investigated the effects of ECM protein density on adipokine secretion and insulin signaling in adipocytes. To this end, 3T3-L1 adipocytes were cultured on the surface of polyacrylamide gels that were coated with gradient densities of a collagen type I and fibronectin mixture. We found that high density ECM causes a decrease in insulin signaling and adiponectin secretion, whereas the secretion of monocyte chemoattractant protein-1 (MCP-1) was increased via the activation of nuclear factor-κB (NF-κB). These results indicate that the density of the ECM directly regulates the inflammatory response and insulin sensitivity of adipocytes.Structured summary: MINT-7992217: Irs1 (uniprotkb:P35569) physically interacts (MI:0915) with phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha (uniprotkb:P26450) by anti bait coimmunoprecipitation (MI:0006)

Identification of ptpro as a novel target gene of Wnt signaling and its potential role as a receptor for Wnt - Uncorrected Proof

Minseong Kim, Hanjun Kim, Eek-hoon Jho — 2010-08-30

Abstract: Wnt/β-catenin signaling plays critical roles in embryonic development and tissue homeostasis in adults by controlling the expression of target genes. We found that expression of ptpro, which encodes a protein tyrosine phosphatase receptor type O (PTPRO), was induced by Wnt/β-catenin signaling in a T cell factor/lymphoid enhancer factor dependent manner. Biochemical assays found that PTPRO interacted with Wnt via its extracellular domain. In addition, ectopic expression of this extracellular domain inhibited Wnt-mediated reporter activity. These results suggest that ptpro is a target gene of Wnt/β-catenin signaling and that PTPRO may function as a novel receptor for Wnt.Structured summary: MINT-7992076: Ptpro (uniprotkb:Q7TSY7) physically interacts (MI:0915) with Wnt3a (uniprotkb:P27467) by anti tag coimmunoprecipitation (MI:0007)MINT-7992094: Ptpro (uniprotkb:Q7TSY7) binds (MI:0407) to Wnt-3a (uniprotkb:P27467) by cross-linking study (MI:0030)

Lysophosphatidic acid stimulates gastric cancer cell proliferation via ERK1-dependent upregulation of sphingosine kinase 1 transcription - Uncorrected Proof

2010-08-30

Abstract: In MKN1 gastric cancer cells, lysophosphatidic acid (LPA) upregulates expression of sphingosine kinase 1 (SphK1) and its downregulation or inhibition suppresses LPA mediated proliferation. Although LPA activates numerous signaling pathways downstream of its receptors, including extracellular-signal-regulated kinase 1/2, p38, JNK, and Akt, and the transactivation of the epidermal growth factor receptor, pharmacological and molecular approaches demonstrated that only activation of ERK1, in addition to the CCAAT/enhancer-binding protein β transcription factor, is involved in transcriptional upregulation of SphK1 by LPA. Our data implicate ERK1 as an important mediator of LPA signaling leading to upregulation of SphK1 and point to SphK1 and sphingosine-1-phosphate production as potential therapeutic targets in gastric cancer.

Activation of human monocytes by a formyl peptide receptor 2-derived pepducin - Uncorrected Proof

2010-08-30

Abstract: We synthesized and investigated the effect of formyl peptide receptor 2 (FPR2)-derived pepducins in human monocytes. The FPR2-based cell-penetrating lipopeptide, “pepducin” (F2pal-16), stimulated intracellular calcium increase in human monocytes via pertussis toxin (PTX)-sensitive G-protein and phospholipase C (PLC) activity. From a functional aspect, we showed that F2pal-16 stimulated monocyte chemotaxis. F2pal-16 also stimulated the generation of superoxide anion in human monocytes. Moreover, F2pal-16 dramatically increased the production of several kinds of pro-inflammatory cytokines (CXCL8, CCL2, IL-1β and TNF-α) in human monocytes via NF-κB activation. Since FPR2 plays an important role in immune responses, F2pal-16 can serve as a useful reagent for the study of FPR2-mediated immune modulation.

Knockdown of apoptosis signal-regulating kinase 1 modulates basal glycogen synthase kinase-3β kinase activity and regulates cell migration - Corrected Proof

Kyung Tae Noh, Ssang-Goo Cho, Eui-Ju Choi — 2010-08-26

Abstract: GSK-3β is a basally active kinase. Axin forms a complex with GSK-3β and β-catenin; this complex promotes the GSK-3β-dependent phosphorylation of β-catenin, thereby inducing its degradation. However, the inhibition of GSK-3β provokes cell migration via the dysregulation of β-catenin. In this study, we determined that the level of apoptosis signal-regulating kinase 1 (ASK1) was lower in a metastatic breast cancer cell line, compared to that of non-metastatic cancer cell lines and the knockdown of ASK1 not only induces β-catenin activation via the inhibition of GSK-3β and collapsing the subsequent protein complex by regulating Axin dynamics, but also stimulates cell migration. Together, the blockage of the GSK-3β–β-catenin pathway resulting from the knockdown of ASK1 modulates the migration of breast cancer cells.

A model for signaling specificity of Wnt/Frizzled combinations through co-receptor recruitment - Corrected Proof

Folkert Verkaar, Guido J.R. Zaman — 2010-08-26

Abstract: Wnts control mammalian developmental morphogenesis and are critical for adult stem cell maintenance. Wnts initiate several intracellular signaling cascades, such as Wnt/β-catenin-, Wnt/Ca2+- and Wnt/ROR2-signaling. Signaling preference of Wnts for these various pathways is thought to depend on the repertoire of receptors present on recipient cells. Here, we propose a further refinement of this receptor model and hypothesize that Wnt signaling specificity depends on co-receptor recruitment upon binding of Wnt to Frizzled receptor molecules. In this model, recruitment of LRP5/6 leads to activation of Wnt/β-catenin signaling, whereas signaling through other pathways is mediated by recruiting ROR2.

Pseudomonas syringae infection triggers de novo synthesis of phytosphingosine from sphinganine in Arabidopsis thaliana - Corrected Proof

Markus Peer, Martin Stegmann, Martin J. Mueller, Frank Waller — 2010-08-23

Abstract: Sphingolipids are important membrane components and also regulate cell proliferation and apoptosis. We detected a fast increase of the free sphingobase t18:0 (phytosphinganine) in Arabidopsis leaves after inoculation with an avirulent strain of the bacterial pathogen Pseudomonas syringae pathovar tomato, characterized by host cell death reactions. The induction of phytosphinganine was more transient in virulent interactions lacking cell death reactions, suggesting a positive role of t18:0 in the plants’ response to pathogens, e.g. the hypersensitive response. In the mutant sphingobase hydroxylase 1 (sbh1-1), Pseudomonas induced elevated free d18:0 levels. As total t18:0 contents (after hydrolysis of ceramides) were not reduced in sbh1-1, the pathogen-triggered t18:0 increase most likely results from de novo synthesis from d18:0 which would require SBH1.

GPR48-induced keratinocyte proliferation occurs through HB-EGF mediated EGFR transactivation - Accepted Manuscript

2010-08-23

Abstract: GPR48 can mediate keratinocyte proliferation and migration. Our investigations showed that AG1478, an inhibitor of EGFR tyrosine kinase, could block GPR48-mediated cellular processes. AG1478 treatment of Gpr48+/+ cells also decreased phosphorylation of EGFR, ERK and STAT3. Subsequent screening using conditioned media immunodepleted of EGFR ligands identified HB-EGF as the ligand responsible for phosphorylation of EGFR, ERK and STAT3. HB-EGF was reduced in Gpr48-/- cell culture medium, but its addition restored the phosphorylation of EGFR, ERK, STAT3, as well as cell proliferation. Confirmation that GPR48 mediates EGFR signaling pathway through HB-EGF was subsequently performed using an inhibitor of HB-EGF.

Epitope tag-induced synthetic lethality between cohesin subunits and Ctf7/Eco1 acetyltransferase - Corrected Proof

Marie E. Maradeo, Robert V. Skibbens — 2010-08-20

Abstract: Ctf7/Eco1-dependent acetylation of Smc3 is essential for sister chromatid cohesion. Here, we use epitope tag-induced lethality in cells diminished for Ctf7/Eco1 activity to map cohesin architecture in vivo. Tagging either Smc1 or Mcd1/Scc1, but not Scc3/Irr1, appears to abolish access to Smc3 in ctf7/eco1 mutant cells, suggesting that Smc1 and Smc3 head domains are in direct contact with each other and also with Mcd1/Scc1. Thus, cohesin complexes may be much more compact than commonly portrayed. We further demonstrate that mutation in ELG1 or RFC5 anti-establishment genes suppress tag-induced lethality, consistent with the notion that the replication fork regulates Ctf7/Eco1.

A novel Aspergillus oryzae esterase that hydrolyzes 4-hydroxybenzoic acid esters - Corrected Proof

Takuya Koseki, Koji Mihara, Tetsuya Murayama, Yoshihito Shiono — 2010-08-20

Abstract: In this study we report the biochemical characterization of a hypothetical protein from Aspergillus oryzae exhibiting sequence identity with feruloyl esterase and tannase from the genus Aspergillus. The purified recombinant protein showed a hydrolytic activity toward the ethyl, propyl, or butyl esters of 4-hydroxybenzoic acid, but did not show feruloyl esterase or tannase activity. Finally, the enzyme decreased the antimicrobial activity of parabens against A. oryzae via hydrolysis of the ester bond present in butyl 4-hydroxybenzoic acid.

Receptors and signaling mechanisms for B-lymphocyte activation, proliferation and differentiation – Insights from both in vivo and in vitro approaches - Uncorrected Proof

2010-08-20

Abstract: During the last three decades, a number of B-lymphocyte specific surface antigens have been defined some of which may also show activation/differentiation specific expression. Here, we review the various signaling events and the receptor-ligand interactions for B-cell development, activation and differentiation. Our discussion and presentation include reviewing the in vivo and in vitro mechanisms. Focus is on the experiments that give us valuable insights into the B cell signaling mechanisms in vitro. Three significant pathways in B-cell development – c-Kit, FLT-3 and IL-7 signaling pathways are elucidated upon. Both antigen dependent and antigen independent mechanisms of B cell stimulation are also reviewed.

Building arks for tRNA: Structure and function of the Arc1p family of non-catalytic tRNA-binding proteins - Corrected Proof

Eleftherios Karanasios, George Simos — 2010-08-20

Abstract: Following the intricate architecture of the eukaryotic cell, protein synthesis involves formation of many macromolecular assemblies, some of which are composed by tRNA-aminoacylation enzymes. Protein–protein and protein–tRNA interactions in these complexes can be facilitated by non-catalytic tRNA-binding proteins. This review focuses on the dissection of the molecular, structural and functional properties of a particular family of such proteins: yeast Arc1p and its homologues in prokaryotes and higher eukaryotes. They represent paradigms of the strategies employed for the organization of sophisticated and dynamic nanostructures supporting spatio-temporal cellular organization.

Alternative splicing of genes during neuronal differentiation of NT2 pluripotential human embryonal carcinoma cells - Corrected Proof

Ai Wakamatsu, Jun-ichi Imai, Shinya Watanabe, Takao Isogai — 2010-08-20

Abstract: We analyzed the mRNA diversity of genes after inducing neuronal differentiation in human NT2 teratocarcinoma cells using all-trans retinoic acid (RA). DNA microarray analyses of cells treated with RA identified 358 RA-responsive genes. mRNA diversity analysis revealed that 274 genes produced multiple protein-coding transcripts by alternative splicing. Among these 274 genes, we chose 26 genes that showed AS in their C-terminus and 12 transcription factor genes for further analysis. By using transcript-specific primers, we performed quantitative real-time PCR analysis to examine the expression profiles of all the protein-coding transcripts. Consequently, we identified genes which showed different RA-induced changes in the expression of their protein-coding transcripts.

Induction of growth arrest by miR-542-3p that targets survivin - Corrected Proof

2010-08-20

Abstract: Survivin is a protein which functions as a mitotic regulator as well as apoptosis inhibitor. In this study, we show that introduction of synthetic miR-542-3p mimetic reduced both mRNA and protein levels of survivin. In A549 cells, luciferase reporter assay revealed that miR-542-3p targeted predicted binding sites in the 3′-untranslated region (3′-UTR) of survivin. We also demonstrate that ectopic expression of miR-542-3p inhibited cell proliferation by inducing Gap 1 (G1) and Gap 2/Mitosis (G2/M) cell cycle arrest. Collectively, these results suggest that survivin is a direct target of miR-542-3p and growth inhibition by miR-542-3p may have a potential utility as an anti-cancer therapy.

The FEBS Letters SDA corpus: A collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community - Corrected Proof

Florian Leitner, Martin Krallinger, Gianni Cesareni, Alfonso Valencia — 2010-08-20

Establishing the interactome, a simplified but complete representation of the functional protein mesh, is a prerequisite for any attempt to model cell physiology . Protein interaction databases such as MINT , IntAct , DIP , or BioGRID strive to recapture the information published in a human readable format in scientific journals and to organize it in a structure that can be understood by a computer. However, this process is time-consuming and databases cannot keep up with the steadily growing amount of protein interaction information published in the scientific literature .

DNA methylation systems and targets in plants - Corrected Proof

Peter Meyer — 2010-08-18

Abstract: Plants contain three distinct DNA methyltransferase types that are responsible for the establishment and maintenance of cytosine methylation patterns at heterochromatic and euchromatic target regions. RNA transcripts play an important role in recruiting DNA methylation systems to specific loci, where methylation patterns are controlled by distinct epigenetic pathways that often work co-operatively and in competition with demethylation functions. DNA methylation patterns are faithfully propagated by maintenance systems that involve re-enforcing feedback effects between DNA methylation and histone marks. Our detailed knowledge about the composition of DNA methylation patterns is contrasted by a poorer understanding of the variability of DNA methylation and its contribution to gene regulation, genome evolution and adaptation to environmental changes.

ATR-FTIR study of the protonation states of the Glu residue in the multicopper oxidases, CueO and bilirubin oxidase - Corrected Proof

2010-08-18

Abstract: Redox-induced protonation state changes of the Glu residue in the multicopper oxidases, CueO and bilirubin oxidase (BO), were studied by attenuated total reflectance-Fourier transform infrared spectroscopy. By monitoring IR bands of the carboxylic acid CO stretch in the wild-type and Glu-to-Gln mutant enzymes the Glu506 of CueO (Glu463 of BO) was found to be unprotonated in the oxidised and protonated in the reduced forms. The results provided direct evidence for proton uptake by the Glu, suggesting it plays a key role in the proton donation to the activated oxygen species in the catalytic cycle.

NADH oxidase activity of Bacillus subtilis nitroreductase NfrA1: Insight into its biological role - Corrected Proof

2010-08-18

Abstract: NfrA1 nitroreductase from the Gram-positive bacterium Bacillus subtilis is a member of the NAD(P)H/FMN oxidoreductase family. Here, we investigated the reactivity, the structure and kinetics of NfrA1, which could provide insight into the unclear biological role of this enzyme. We could show that NfrA1 possesses an NADH oxidase activity that leads to high concentrations of oxygen peroxide and an NAD+ degrading activity leading to free nicotinamide. Finally, we showed that NfrA1 is able to rapidly scavenge H2O2 produced during the oxidative process or added exogenously.Structured summary: MINT-7990140: nfrA1 (uniprotkb:P39605) and nfrA1 (uniprotkb:P39605) bind (MI:0407) by X-ray crystallography (MI:0114)

Corrigendum to “Cytokinesis and cancer” [FEBS Lett. 584 (2010) 2652–2661] - Corrected Proof

Antonia P. Sagona, Harald Stenmark — 2010-08-17

In Table 1 and the second paragraph of Section 2.2, the expression “survinin” should read “survivin”.

ARF-dependent regulation of ATM and p53 associated KZNF (Apak) protein activity in response to oncogenic stress - Corrected Proof

2010-08-16

Abstract: The KRAB-type zinc-finger protein Apak (ATM and p53 associated KZNF protein) specifically suppresses p53-mediated apoptosis. Upon DNA damage, Apak is phosphorylated and inhibited by ATM kinase, resulting in p53 activation. However, how Apak is regulated in response to oncogenic stress remains unknown. Here we show that upon oncogene activation, Apak is inhibited in the tumor suppressor ARF-dependent but ATM-independent manner. Oncogene-induced ARF protein directly interacts with Apak and competes with p53 to bind to Apak, resulting in Apak dissociation from p53. Thus, Apak is differentially regulated in the ARF and ATM-dependent manner in response to oncogenic stress and DNA damage, respectively.Structured summary: MINT-7989670: p53 (uniprotkb:P04637) binds (MI:0407) to APAK (uniprotkb:Q8TAQ5) by pull down (MI:0096)MINT-7989812: HDM2 (uniprotkb:Q00987) physically interacts (MI:0915) with ARF (uniprotkb:Q8N726-1) by anti bait coimmunoprecipitation (MI:0006)MINT-7989603, MINT-7989626: APAK (uniprotkb:Q8TAQ5) physically interacts (MI:0915) with ARF (uniprotkb:Q8N726-1) by anti bait coimmunoprecipitation (MI:0006)MINT-7989653: ARF (uniprotkb:Q8N726-1) binds (MI:0407) to APAK (uniprotkb:Q8TAQ5) by pull down (MI:0096)MINT-7989686, MINT-7989705, MINT-7989747:APAK (uniprotkb:Q8TAQ5) physically interacts (MI:0915) with ARF (uniprotkb:Q8N726-1) by anti tag coimmunoprecipitation (MI:0007)MINT-7989724: APAK (uniprotkb:Q8TAQ5) physically interacts (MI:0914) with ARF (uniprotkb:Q8N726-1) and p53 (uniprotkb:P04637) by anti tag coimmunoprecipitation (MI:0007)MINT-7989635: ARF (uniprotkb:Q8N726-1) and APAK (uniprotkb:Q8TAQ5) colocalize (MI:0403) by fluorescence microscopy (MI:0416)MINT-7989584, MINT-7989773: APAK (uniprotkb:Q8TAQ5) physically interacts (MI:0915) with p53 (uniprotkb:P04637) by anti tag coimmunoprecipitation (MI:0007)

Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2 - Corrected Proof

2010-08-13

Abstract: The BET family proteins recognize acetylated chromatin through their two bromodomains, acting as transcriptional activators or tethering viral genomes to the mitotic chromosomes of their host. The structural mechanism for how the N-terminal bromodomain of human BRD2 (BRD2-BD1) deciphers the mono-acetylated status of histone H4 tail was recently reported. Here we show the crystal structure of the second bromodomain of BRD2 (BRD2-BD2) in complex with the di-acetylated histone H4 tail (H4K5ac/K12ac). To our surprise, a single K5ac/K12ac peptide interacts with two BRD2-BD2 molecules simultaneously: the K5ac residue binds to one BRD2-BD2 molecule while the K12ac residue binds to another. These results provide a structural basis for the recognition of two different patterns of the histone acetylation status by a single bromodomain.Structured summary: MINT-7989882, MINT-7989824, MINT-7989846, MINT-7989865: H4 (uniprotkb:P62805) binds (MI:0407) to BRD2 (uniprotkb:P25440) by surface plasmon resonance (MI:0107) MINT-7989539: H4 (uniprotkb:P62805) and BRD2 (uniprotkb:P25440) bind (MI:0407) by X-ray crystallography (MI:0114)

The JNK inhibitor SP600125 enhances dihydroartemisinin-induced apoptosis by accelerating Bax translocation into mitochondria in human lung adenocarcinoma cells - Corrected Proof

Ying-Ying Lu, Tong-Sheng Chen, Xiao-Ping Wang, Jun-Le Qu, Min Chen — 2010-08-13

Abstract: The C-Jun N-terminal Kinase (JNK) inhibitor SP600125 is widely used to inhibit the JNK-mediated Bax activation and cell apoptosis. However, this report demonstrates that SP600125 synergistically enhances the dihydroartemisinin (DHA)-induced human lung adenocarcinoma cell apoptosis by accelerating Bax translocation and subsequent intrinsic apoptotic pathway involving mitochondrial membrane depolarization, cytochrome c release, caspase-9 and caspase-3 activation. The dynamical analysis of GFP-Bax mobility inside single living cells using fluorescence recovery after photobleaching revealed that SP600125 aggravated the DHA-induced decrease of Bax mobility and Bax translocation. These results for the first time present a novel pro-apoptotic action of SP600125 in DHA-induced apoptosis.

DJ-1, an oncogene and causative gene for familial Parkinson’s disease, is essential for SV40 transformation in mouse fibroblasts through up-regulation of c-Myc - Corrected Proof

Yun Chul Kim, Hirotake Kitaura, Sanae M.M. Iguchi-Ariga, Hiroyoshi Ariga — 2010-08-12

Abstract: Simian virus 40 (SV40) is a tumor virus and its early gene product large T-antigen (LT) is responsible for the transforming activity of SV40. Parkinson’s disease causative gene DJ-1 is also a ras-dependent oncogene, but the mechanism of its oncogene function is still not known. In this study, we found that there were no transformed foci when fibroblasts from DJ-1-knockout mice were transfected with LT. We also found that DJ-1 directly bound to LT and that the expression level of c-Myc in transformed cells was parallel to that of DJ-1. These findings indicate that DJ-1 is essential for SV40 transformation.Structured summary: MINT-7988969: DJ-1 (uniprotkb:Q99497) binds (MI:0407) to LT SV40 (uniprotkb:P03070) by pull down (MI:0096) MINT-7988948: LT SV40 (uniprotkb:P03070) physically interacts (MI:0914) with DJ-1 (uniprotkb:Q99LX0) and p53 (uniprotkb:P02340) by anti bait coimmunoprecipitation (MI:0006)

The double mutation ΔL6MW241F in PsbO, the photosystem II manganese stabilizing protein, yields insights into the evolution of its structure and function - Corrected Proof

Hana Popelkova, Alan Commet, Charles F. Yocum — 2010-08-12

Abstract: The W241F mutation in spinach manganese-stabilizing protein (PsbO) decreases binding to photosystem II (PSII); its thermostability is increased and reconstituted activity is lower [Wyman et al. (2008) Biochemistry 47, 6490–6498]. The results reported here show that W241F cannot adopt a normal solution structure and fails to reconstitute efficient Cl− retention by PSII. An N-terminal truncation of W241F, producing the ΔL6MW241F double mutant that resembles some features of cyanobacterial PsbO, significantly repairs the defects in W241F. Our data suggest that the C-terminal F→W mutation likely evolved in higher plants and green algae in order to preserve proper PsbO folding and PSII binding and assembly, which promotes efficient Cl− retention in the oxygen-evolving complex.

Insights into the genomic features and evolutionary impact of the genes configuring duplicated pseudogenes in human - Corrected Proof

Kamalika Sen, Soumita Podder, Tapash Chandra Ghosh — 2010-08-12

Abstract: Pseudogenes, regarded as ‘genomic fossils’, are DNA sequences resembling functional genes in perspective of sequence homology but completely non-functional. In this study, we explored the unique characteristic features of human genes, configuring classical duplicated pseudogenes. We found that progenitors of duplicated pseudogenes are characterized by a high expressivity, and ability to encode hub-proteins in association with a high evolutionary rate. Such unusual features are endorsed by longer protein length, elevated CpG content, and a high recombination rate. The non-functionalization of their duplicated copies can be attributed to the overabundance of gene paralog number in concert with functional redundancy.

Current inhibition of human EAG1 potassium channels by the Ca2+ binding protein S100B - Corrected Proof

Nirakar Sahoo, Jessica Tröger, Stefan H. Heinemann, Roland Schönherr — 2010-08-12

Abstract: Voltage-dependent human ether à go-go (hEAG1) potassium channels are implicated in neuronal signaling as well as in cancer cell proliferation. Unique sensitivity of the channel to intracellular Ca2+ is mediated by calmodulin (CaM) binding to the intracellular N- and C-termini of the channel. Here we show that application of the acidic calcium-binding protein S100B to inside-out patches of Xenopus oocytes causes Ca2+-dependent inhibition of expressed hEAG1 channels. Protein pull-down assays and fluorescence correlation spectroscopy (FCS) revealed that S100B binds to hEAG1 and shares the same binding sites with CaM. Thus, S100B is a potential alternative calcium sensor for hEAG1 potassium channels.Structured summary: MINT-7988123: CaM (uniprotkb:P62158) and EAG1 alpha (uniprotkb:O95259) physically interact (MI:0915) by competition binding (MI:0405)MINT-7988019, MINT-7988052: EAG1 alpha (uniprotkb:O95259) binds (MI:0407) to s100B (uniprotkb:P02638) by pull down (MI:0096)MINT-7988074: EAG1 alpha (uniprotkb:O95259) and s100B (uniprotkb:P02638) physically interact (MI:0915) by competition binding (MI:0405)MINT-7988100:CaM (uniprotkb:P62158) and EAG1 alpha (uniprotkb:O95259) bind (MI:0407) by fluorescence correlation spectroscopy (MI:0052).

Dysregulation of microRNAs in cancer: Playing with fire - Corrected Proof

Sonia A. Melo, Manel Esteller — 2010-08-11

Abstract: MicroRNAs have emerged as key post-transcriptional regulators of gene expression, involved in various physiological and pathological processes. It was found that several miRNAs are directly involved in human cancers, including lung, breast, brain, liver, colon cancer and leukemia. In addition, some miRNAs may function as oncogenes or tumor suppressors in tumor development. Furthermore, a widespread down-regulation of miRNAs is commonly observed in human cancers and promotes cellular transformation and tumorigenesis . More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites, frequently amplified or deleted in human cancer, suggesting an important role in malignant transformation. A better understanding of the miRNA regulation and misexpression in cancer may ultimately yield further insight into the molecular mechanisms of tumorigenesis and new therapeutic strategies may arise against cancer. Here, we discuss the occurrence of the deregulated expression of miRNAs in human cancers and their importance in the tumorigenic process.

POSH2 is a RING finger E3 ligase with Rac1 binding activity through a partial CRIB domain - Corrected Proof

Satu Kärkkäinen, Maarten van der Linden, G. Herma Renkema — 2010-08-09

Abstract: The Plenty of SH3 domains protein (POSH) is an E3 ligase and a scaffold in the JNK mediated apoptosis, linking Rac1 to downstream components.We here describe POSH2 which was identified from a p21-activated kinase 2 (PAK2) interactor screen. POSH2 is highly homologous with other members of the POSH family; it contains four Src homology 3 (SH3) domains and a RING finger domain which confers E3 ligase activity to the protein. In addition POSH2 contains an N-terminal extension which is conserved among its mammalian counterparts. POSH2 interacts with GTP-loaded Rac1. We have mapped this interaction to a previously unrecognized partial Cdc42/Rac1-interactive binding domain.Structured summary: MINT-7987761: POSH1 (uniprotkb:Q9HAM2) physically interacts (MI:0915) with Ubiquitin (uniprotkb:P62988) by anti tag coimmunoprecipitation (MI:0007)MINT-7987932: PAK2 (uniprotkb:Q13177) binds (MI:0407) to CDC42 (uniprotkb:Q07912) by solid phase assay (MI:0892)MINT-7987908: POSH1 (uniprotkb:Q9HAM2) binds (MI:0407) to Rac1 (uniprotkb:P63000) by solid phase assay (MI:0892)MINT-7987880: POSH2 (uniprotkb:Q8TEJ3) binds (MI:0407) to Rac1 (uniprotkb:P63000) by solid phase assay (MI:0892)MINT-7987734: POSH2 (uniprotkb:Q8TEJ3) physically interacts (MI:0915) with Ubiquitin (uniprotkb:P62988) by anti tag coimmunoprecipitation (MI:0007)MINT-7987779, MINT-7987804, MINT-7987824, MINT-7987838, MINT-7987853: Rac1 (uniprotkb:P63000) physically interacts (MI:0915) with POSH2 (uniprotkb:Q8TEJ3) by anti tag coimmunoprecipitation (MI:0007)MINT-7987920: PAK2 (uniprotkb:Q13177) binds (MI:0407) to Rac1 (uniprotkb:P63000) by solid phase assay (MI:0892)

Tankyrase-1 assembly to large protein complexes blocks its telomeric function - Corrected Proof

Kaori Hatsugai, Tomokazu Ohishi, Yoshikazu Sugimoto, Hiroyuki Seimiya — 2010-08-09

Abstract: Tankyrase-1 poly(ADP-ribosyl)ates the telomere-binding protein TRF1. This post-translational modification dissociates TRF1 from telomeres, enhancing telomerase-mediated telomere elongation. Tankyrase-1 multimerizes via its sterile alpha motif domain, but its functional implication remains elusive. Here, we found that excessive amounts of tankyrase-1 form punctate nuclear foci. This focus formation depends on both homophilic multimerization and heterophilic protein–protein interaction. These foci are functionally dormant because they do not efficiently release TRF1 from telomeres. Consistently, hyper-overexpression of tankyrase-1 attenuates its ability to elongate telomeres. These observations suggest that tankyrase-1 assembly to large protein complexes masks its telomeric function.Structured summary: MINT-7987689, MINT-7987677: Tankyrase-1 (uniprotkb:O95271) and TRF1 (uniprotkb:P54274) colocalize (MI:0403) by fluorescence microscopy (MI:0416)MINT-7987977: Tankyrase-1 (uniprotkb:O95271) physically interacts (MI:0915) with TRF1 (uniprotkb:P54274) by anti tag coimmunoprecipitation (MI:0007)MINT-7987998: Tankyrase-1 (uniprotkb:O95271) physically interacts (MI:0915) with Tankyrase-1 (uniprotkb:O95271) by anti tag coimmunoprecipitation (MI:0007).

Mast cell signaling: The role of protein tyrosine kinase Syk, its activation and screening methods for new pathway participants - Corrected Proof

Reuben P. Siraganian, Rodrigo O. de Castro, Emilia A. Barbu, Juan Zhang — 2010-08-09

Abstract: The aggregation by antigen of the IgE bound to its high affinity receptor on mast cells initiates a complex series of biochemical events that result in the release of inflammatory mediators. The essential role of the protein tyrosine kinase Syk has been appreciated for some time, and newer results have defined the mechanism of its activation. The use of siRNA has defined the relative contribution of Syk, Fyn and Gab2 to signaling and has made possible a screening study to identify previously unrecognized molecules that are involved in these pathways.

A cytotoxic peptide from a marine sponge exhibits ion channel activity through vectorial-insertion into the membrane - Corrected Proof

Masayuki Iwamoto, Hirofumi Shimizu, Ikunobu Muramatsu, Shigetoshi Oiki — 2010-08-09

Abstract: A cytotoxic peptide, polytheonamide B (pTB), from marine sponge was examined for cytotoxic spectrum and specific activity to mammalian cells was demonstrated. pTB is composed of alternative D- and L-amino acid residues throughout the 48-mer peptide. This suggests the formation of a β-helix similar to gramicidin channels. Planar bilayer experiments revealed that pTB forms monovalent cation-selective channels, being compatible with the inner pore diameter of ∼4Å for a β-helical structure. pTB penetrated vectorially into the membrane, formed a channel by means of a single molecule, and remained in the membrane. These functional properties may account for specific cytotoxic activity.

Reporter gene expression at single-cell level characterized with real-time RT-PCR, chemiluminescence, fluorescence, and electrochemical imaging - Corrected Proof

2010-08-09

Abstract: mRNA from single cells was quantified using real-time RT-PCR after recording the address and reporter protein activity with chemiluminescence, fluorescence, and electrochemical techniques, using luciferase, green fluorescent protein, and secreted alkaline phosphatase. mRNA copy number ranging from below 103 to 107 in single cells showed a lognormal distribution for both externally introduced reporter genes and internally expressed genes. The fluctuation in the gene expression decreased with the increase of the number of cells picked but did not decrease with the increase of mRNA copy number per cell. We found that the correlation coefficients for mRNA and protein expression in logarithmic plot at single-cell level were much lower than 1.00.

Nuclear EGFR shuttling induced by ionizing radiation is regulated by phosphorylation at residue Thr654 - Corrected Proof

2010-08-06

Abstract: Nuclear localisation of EGFR is associated with treatment resistance of tumor cells. The aim of this study was to identify molecular targets to block nuclear shuttling of EGFR. Mutation of Thr654, located within the putative EGFR NLS demonstrated that phosphorylation of this residue is essential for nuclear EGFR shuttling following irradiation. Deletion of Thr654 blocked nuclear transport of EGFR, whereas mutation to Glu increased shuttling. Treatment with a peptide, corresponding to the phosphorylated NLS, abolished nuclear EGFR transport and reduced radiation-induced activation of DNA-PK, essential for DNA-repair. In accordance with that, lack of nuclear EGFR increased residual DNA damage in tumor cells and reduced cellular survival following irradiation. Blockage of nuclear EGFR shuttling may be a new strategy to fight treatment resistance.Structured summary: MINT-7987956: Karyopherin alpha (uniprotkb:P52294) physically interacts (MI:0915) with EGFR (uniprotkb:P00533) by anti bait coimmunoprecipitation (MI:0006)

Cyclic cytidine 3′,5′-monophosphate (cCMP) signals via cGMP kinase I - Corrected Proof

2010-08-05

Abstract: We analysed the function and intracellular signalling of the cyclic pyrimidinic nucleotide cCMP. The membrane-permeable cCMP analogue dibutyryl-cCMP mediated mouse aorta relaxation. cCMP activated purified cGMP-dependent protein kinase (cGK) Iα and Iβ and stimulated cGK in aorta lysates. cCMP-induced relaxation was abolished in cGKI-knockout tissue. Additionally, deletion of inositol–trisphosphate receptor associated cGKI substrate (IRAG) suppressed cCMP-mediated relaxation. Signalling of cCMP via cGKI/IRAG appears to be of broader physiological importance because cCMP-mediated inhibition of platelet aggregation was absent in cGKI- and IRAG-deficient platelets. These results demonstrate that cCMP acts as intracellular messenger molecule, most unexpectedly utilizing the cGMP signal transduction pathway.

Isolation of a point-mutated p47 lacking binding affinity to p97ATPase - Corrected Proof

Yayoi Kaneko, Kaori Tamura, Go Totsukawa, Hisao Kondo — 2010-08-05

Abstract: p47, a p97-binding protein, functions in Golgi membrane fusion together with p97 and VCIP135, another p97-binding protein. We have succeeded in creating p47 with a point mutation, F253S, which lacks p97-binding affinity. p47 mapping experiments revealed that p47 had two p97-binding regions and the F253S mutation occurred in the first p97-binding site. p47(F253S) could not form a complex with p97 and did not caused any cisternal regrowth in an in vitro Golgi reassembly assay. In addition, mutation corresponding to the p47 F253S mutation in p37 and ufd1 also abolished their binding ability to p97.Structured summary: MINT-7987189, MINT-7987207, MINT-7987303: p47 (uniprotkb:O35987) binds (MI:0407) to p97 (uniprotkb:Q01853) by pull down (MI:0096)MINT-7987226: p97 (uniprotkb:P46462) binds (MI:0407) to p47 (uniprotkb:O35987) by pull down (MI:0096)MINT-7987348: p97 (uniprotkb:P46462) physically interacts (MI:0915) with Ufd1 (uniprotkb:P70362) by pull down (MI:0096)MINT-7987264: p97 (uniprotkb:P46462) and p47 (uniprotkb:O35987) bind (MI:0407) by competition binding (MI:0405)MINT-7987326: p97 (uniprotkb:P46462) binds (MI:0407) to p37 (uniprotkb:Q0KL01) by pull down (MI:0096)

Molecular characterization of β1,4-galactosyltransferase 7 genetic mutations linked to the progeroid form of Ehlers–Danlos syndrome (EDS) - Corrected Proof

2010-08-05

Abstract: β1,4-Galactosyltransferase 7 (β4GalT7) is a key enzyme initiating glycosaminoglycan (GAG) synthesis. Based on in vitro and ex vivo kinetics studies and structure-based modelling, we molecularly characterized β4GalT7 mutants linked to the progeroid form of Ehlers–Danlos syndrome (EDS), a severe connective tissue disorder. Our results revealed that loss of activity upon L206P substitution due to altered protein folding is the primary cause for the GAG synthesis defect in patients carrying the compound A186D and L206P mutations. We showed that R270C substitution strongly reduced β4GalT7 affinity towards xyloside acceptor, thus affecting GAG chains formation. This study establishes the molecular basis for β4GalT7 defects associated with altered GAG synthesis in EDS.

Extracellular signal-regulated kinase (ERK) participates in the hypercapnia-induced Na,K-ATPase downregulation - Corrected Proof

2010-08-05

Abstract: Hypercapnia has been shown to impair alveolar fluid reabsorption (AFR) by decreasing Na,K-ATPase activity. Extracellular signal-regulated kinase pathway (ERK) is activated under conditions of cellular stress and has been known to regulate the Na,K-ATPase. Here, we show that hypercapnia leads to ERK activation in a time-dependent manner in alveolar epithelial cells (AEC). Inhibition of ERK by U0126 or siRNA prevented both the hypercapnia-induced Na,K-ATPase endocytosis and impairment of AFR. Moreover, ERK inhibition prevented AMPK activation, a known modulator of hypercapnia-induced Na,K-ATPase endocytosis. Accordingly, these data suggest that hypercapnia-induced Na,K-ATPase endocytosis is dependent on ERK activation in AEC and that ERK plays an important role in hypercapnia-induced impairment of AFR in rat lungs.

The correlation coefficient of GC content of the genome-wide genes is positively correlated with animal evolutionary relationships - Corrected Proof

2010-08-05

Abstract: In this study, we present a new method for evaluating animal evolutionary relationships. We used the GC% levels of genome-wide genes to determine the correlation between the GC% content and evolutionary relationship. The correlation coefficients of the GC% content of the orthologous genes of the paired animal species were calculated for a total of 21 species, and the evolutionary branching dates of these 21 species were derived from fossil records. The correlation coefficient of the GC% content of the orthologous genes of the species pair under study served as an indicator of their evolutionary relationship. Moreover, there was a decreasing linear relationship between the correlation coefficient and evolutionary branching date (R2=0.930).

S. Prakash Datta (1920–2010) - Corrected Proof

J. Mowbray — 2010-08-04

Professor Satya Prakash Datta, the founding Managing Editor of FEBS letters, died peacefully at his home in Chiswick on 12th May a few days after he had celebrated his 90th birthday in fine style with a group of family and friends.

S. Prakash Datta (1920–2010) - Corrected Proof

Giorgio Semenza — 2010-08-03

Very likely, I belong to the small group of people who have known Prakash Datta longer than most. We met the first time during the first FEBS meeting (London, 1964) i.e. nearly half-a-century ago.

A distinct subset of podoplanin (gp38) expressing F4/80+ macrophages mediate phagocytosis and are induced following zymosan peritonitis - Corrected Proof

2010-08-02

Abstract: Macrophages are important tissue resident cells that regulate the dynamics of inflammation. However, they are strikingly heterogeneous. During studies looking at podoplanin (gp38) expression on stromal cells in the murine spleen and peritoneal cavity we unexpectedly discovered that podoplanin was expressed on a subset of F4/80+ macrophages; a subset which we have termed fibroblastic macrophages (FM). These cells function as phagocytes in vitro as measured by bead mediated phagocytosis assays. FM also exist at high frequency in the peritoneal cavity and in zymosan induced peritonitis in vivo. These FM represent a unique subgroup of F4/80+ macrophages and their presence in the inflamed peritoneum suggests that they play a role in zymosan induced peritonitis.

Oxazolone-induced over-expression of focal adhesion kinase in colonic epithelial cells of colitis mouse model - Corrected Proof

2010-08-02

Abstract: We examined the change of protein tyrosine kinases (PTKs) expression levels in colonic epithelial cells isolated from mice in which colitis was induced by oxazolone administration, using the monoclonal antibody YK34, which cross-reacts with a wide variety of PTKs. We identified focal adhesion kinase (FAK) and found the expression level increased due to the induction of colitis. Furthermore, we found that there was a positive correlation between FAK expression and the severity of colitis. Also, FAK expression localized in the colonic epithelium but not in the lamina propria, implying FAK functions in epithelial cells during colitis formation and/or wound repairing.

Induction of endosomal/lysosomal pathways in differentiating osteoblasts as revealed by combined proteomic and transcriptomic analyses - Corrected Proof

2010-08-02

Abstract: We have analyzed proteome changes associated with bone-forming osteoblast differentiation by quantitative differential proteomic and transcriptomic analyses using in vitro differentiation model. Sixty nine proteins were found up-regulated (>2-fold) and 18 were down-regulated (<0.5-fold) at protein level. The mRNA levels of these proteins were then analyzed by quantitative real-time PCR combined with clustering analysis. The most prominent cluster with increased protein and mRNA levels contains endosomal and lysosomal proteins, demonstrating the drastic induction of degradative endosomal/lysosomal pathways in osteoblasts. Osteoblasts, therefore, are involved not only in the synthesis but also in the turnover of the extracellular matrix proteins such as collagens.