bluuebunny/crossref_metadata_2025 huggingface dataset:
Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes from a Structural Perspective
Authors: Wedekind Joseph E.
Published: June 2011

Ribozymes are often perceived as part of an antiquated catalytic arsenal hearkening back to a pre-biotic RNA World that was eventually supplanted by proteins. However, recent genome-wide searches have revealed a plethora of new catalytic RNA motifs that appear to be variations on well-known themes. This suggests that ribozymes have continued to evolve in order to fulfill specific, RNA-essential biological niches. Although such ribozymes are small and catalyze one-step phosphodiester-bond scission reactions, ongoing structure and function analyses at the lab bench have demonstrated that RNA has the capacity for a diverse number of reactions such as carbon-carbon bond formation, and tRNA aminoacylation. Here we describe the fundamental structure and metal binding properties of four naturally occurring RNA enzymes: the hammerhead, hairpin, hepatitis delta virus, and glmS metabolite sensing ribozyme. In addition, we discuss the fold and ion coordination of three artificial ribozymes developed to probe the boundaries of RNA catalysis; these include the leadzyme, the flexizyme, and the Diels-Alder ribozyme. Our approach is to relate structure to function with the knowledge of ideal metal-ion coordination geometry that we have derived herein from surveys of high-resolution small molecule structures. An emergent theme is that natural and artificial ribozymes that catalyze single-step reactions often possess a pre-formed active site. Multivalent ions facilitate RNA active site formation, but can also provide Lewis acid functionality that is necessary for catalysis. When metal ion binding isn't possible, ribozymes make due by ionizing their bases, or by recruiting cofactors that augment their chemical functionality.
Ataxia telangiectasia mutated- and Rad3-related kinase drives both the early and the late DNA-damage response to the monofunctional antitumour alkylator S23906
Authors: Soares Daniele G. , Battistella Aude , Rocca Céline J. , Matuo Renata , Henriques João A. P. , Larsen Annette K. , Escargueil Alexandre E.
Published: June 2011

Numerous anticancer agents and environmental mutagens target DNA. Although all such compounds interfere with the progression of the replication fork and inhibit DNA synthesis, there are marked differences in the DNA-damage response pathways they trigger, and the relative impact of the proximal or the distal signal transducers on cell survival is mainly lesion-specific. Accordingly, checkpoint kinase inhibitors in current clinical development show synergistic activity with some DNA-targeting agents, but not with others. In the present study, we characterize the DNA-damage response to the antitumour acronycine derivative S23906, which forms monofunctional adducts with guanine residues in the minor groove of DNA. S23906 exposure is accompanied by specific recruitment of RPA (replication protein A) at replication sites and rapid Chk1 activation. In contrast, neither MRN (Mre11-Rad50-Nbs1) nor ATM (ataxia-telangiectasia mutated), contributes to the initial response to S23906. Interestingly, genetic attenuation of ATR (ATM- and Ras3-related) activity inhibits not only the early phosphorylation of histone H2AX and Chk1, but also interferes with the late phosphorylation of Chk2. Moreover, loss of ATR function or pharmacological inhibition of the checkpoint kinases by AZD7762 is accompanied by abrogation of the S-phase arrest and increased sensitivity towards S23906. These findings identify ATR as a central co-ordinator of the DNA-damage response to S23906, and provide a mechanistic rationale for combinations of S23906 and similar agents with checkpoint abrogators.
Stereospecific reduction of 5β-reduced steroids by human ketosteroid reductases of the AKR (aldo-keto reductase) superfamily: role of AKR1C1–AKR1C4 in the metabolism of testosterone and progesterone via the 5β-reductase pathway
Authors: Jin Yi , Mesaros A. Clementina , Blair Ian A. , Penning Trevor M.
Published: June 2011

Active sex hormones such as testosterone and progesterone are metabolized to tetrahydrosteroids in the liver to terminate hormone action. One main metabolic pathway, the 5β-pathway, involves 5β-steroid reductase (AKR1D1, where AKR refers to the aldo-keto reductase superfamily), which catalyses the reduction of the 4-ene structure, and ketosteroid reductases (AKR1C1–AKR1C4), which catalyse the subsequent reduction of the 3-oxo group. The activities of the four human AKR1C enzymes on 5β-dihydrotestosterone, 5β-pregnane-3,20-dione and 20α-hydroxy-5β-pregnan-3-one, the intermediate 5β-dihydrosteroids on the 5β-pathway of testosterone and progesterone metabolism, were investigated. Product characterization by liquid chromatography–MS revealed that the reduction of the 3-oxo group of the three steroids predominantly favoured the formation of the corresponding 3α-hydroxy steroids. The stereochemistry was explained by molecular docking. Kinetic properties of the enzymes identified AKR1C4 as the major enzyme responsible for the hepatic formation of 5β-tetrahydrosteroid of testosterone, but indicated differential routes and roles of human AKR1C for the hepatic formation of 5β-tetrahydrosteroids of progesterone. Comparison of the kinetics of the AKR1C1–AKR1C4-catalysed reactions with those of AKR1D1 suggested that the three intermediate 5β-dihydrosteroids derived from testosterone and progesterone are unlikely to accumulate in liver, and that the identities and levels of 5β-reduced metabolites formed in peripheral tissues will be governed by the local expression of AKR1D1 and AKR1C1–AKR1C3.
Cyclodextrin, a novel therapeutic tool for suppressing amyloidogenic transthyretin misfolding in transthyretin-related amyloidosis
Authors: Jono Hirofumi , Anno Takayuki , Motoyama Keiichi , Misumi Yohei , Tasaki Masayoshi , Oshima Toshinori , Mori Yoshimasa , Mizuguchi Mineyuki , Ueda Mitsuharu , Shono Makoto , Obayashi Konen , Arima Hidetoshi , Ando Yukio
Published: June 2011

TTR (transthyretin), a β-sheet-rich protein, is the precursor protein of familial amyloidotic polyneuropathy and senile systemic amyloidosis. Although it has been widely accepted that protein misfolding of the monomeric form of TTR is a rate-limiting step for amyloid formation, no effective therapy targeting this misfolding step is available. In the present study, we focused on CyDs (cyclodextrins), cyclic oligosaccharides composed of glucose units, and reported the inhibitory effect of CyDs on TTR amyloid formation. Of various branched β-CyDs, GUG-β-CyD [6-O-α-(4-O-α-D-glucuronyl)-D-glucosyl-β-CyD] showed potent inhibition of TTR amyloid formation. Far-UV CD spectra analysis showed that GUG-β-CyD reduced the conformational change of TTR in the process of amyloid formation. In addition, tryptophan fluorescence and 1H-NMR spectroscopy analyses indicated that GUG-β-CyD stabilized the TTR conformation via interaction with the hydrophobic amino acids of TTR, especially tryptophan. Moreover, GUG-β-CyD exerted its inhibitory effect by reducing TTR deposition in transgenic rats possessing a human variant TTR gene in vivo. Collectively, these results indicate that GUG-β-CyD may inhibit TTR misfolding by stabilizing its conformation, which, in turn, suppresses TTR amyloid formation.
Characterization of DNA-binding activity in the N-terminal domain of the DNA methyltransferase Dnmt3a
Authors: Suetake Isao , Mishima Yuichi , Kimura Hironobu , Lee Young-Ho , Goto Yuji , Takeshima Hideyuki , Ikegami Takahisa , Tajima Shoji
Published: June 2011

The Dnmt3a gene, which encodes de novo-type DNA methyltransferase, encodes two isoforms, full-length Dnmt3a and Dnmt3a2, which lacks the N-terminal 219 amino acid residues. We found that Dnmt3a showed higher DNA-binding and DNA-methylation activities than Dnmt3a2. The N-terminal sequence from residues 1 to 211 was able to bind to DNA, but could not distinguish methylated and unmethylated CpG. Its binding to DNA was inhibited by a major groove binder. Four basic amino acid residues, Lys51, Lys53, Arg177 and Arg179, in the N-terminal region were crucial for the DNA-binding activity. The ectopically expressed N-terminal sequence (residues 1–211) was localized in nuclei, whereas that harbouring mutations at the four basic amino acid residues was also detected in the cytoplasm. The DNA-methylation activity of Dnmt3a with the mutations was suppressed under physiological salt conditions, which is similar that of Dnmt3a2. In addition, ectopically expressed Dnmt3a with mutations, as well as Dnmt3a2, could not be retained efficiently in nuclei on salt extraction. We conclude that the DNA-binding activity of the N-terminal domain contributes to the DNA-methyltransferase activity via anchoring of the whole molecule to DNA under physiological salt conditions.
TTBK2 kinase substrate specificity and the impact of spinocerebellar-ataxia-causing mutations on expression, activity, localization and development
Authors: Bouskila Michale , Esoof Noor , Gay Laurie , Fang Emily H. , Deak Maria , Begley Michael J. , Cantley Lewis C. , Prescott Alan , Storey Kate G. , Alessi Dario R.
Published: June 2011

Mutations that truncate the C-terminal non-catalytic moiety of TTBK2 (tau tubulin kinase 2) cause the inherited, autosomal dominant, SCA11 (spinocerebellar ataxia type 11) movement disorder. In the present study we first assess the substrate specificity of TTBK2 and demonstrate that it has an unusual preference for a phosphotyrosine residue at the +2 position relative to the phosphorylation site. We elaborate a peptide substrate (TTBKtide, RRKDLHDDEEDEAMSIYpA) that can be employed to quantify TTBK2 kinase activity. Through modelling and mutagenesis we identify a putative phosphate-priming groove within the TTBK2 kinase domain. We demonstrate that SCA11 truncating mutations promote TTBK2 protein expression, suppress kinase activity and lead to enhanced nuclear localization. We generate an SCA11-mutation-carrying knockin mouse and show that this leads to inhibition of endogenous TTBK2 protein kinase activity. Finally, we find that, in homozygosity, the SCA11 mutation causes embryonic lethality at embryonic day 10. These findings provide the first insights into some of the intrinsic properties of TTBK2 and reveal how SCA11-causing mutations affect protein expression, catalytic activity, localization and development. We hope that these findings will be helpful for future investigation of the regulation and function of TTBK2 and its role in SCA11.
Procathepsin L secretion, which triggers tumour progression, is regulated by Rab4a in human melanoma cells
Authors: Barbarin Alice , Frade Raymond
Published: June 2011

The switch of human melanoma cell phenotype from non to highly tumorigenic and metastatic is triggered by the increase of procathepsin L secretion, which modifies the tumour microenvironment. The aim of the present study was to identify components involved in the regulation of procathepsin L secretion in melanoma cells. We focused on Rab family members, i.e. Rab3A, Rab4A, Rab4B, Rab5A, Rab8A, Rab11A, Rab27A and Rab33A, which are involved in distinct regulatory pathways. From analysis of mRNA and protein expression of these Rab components and their knockdown by specific siRNAs (small interfering RNAs) it emerged that Rab4A protein is involved in the regulation of procathepsin L secretion. This result was strengthened as procathepsin L secretion was either inhibited by expression of a Rab4A dominant-negative mutant or increased by overexpression of the wild-type Rab4A. Rab4A regulation: (i) discriminates between procathepsin L secretion and expression of intracellular cathepsin L forms; (ii) did not modify other Rab proteins and GAPDH (glyceraldehyde-3-phosphate dehydrogenase) expression, or IL-8 (interleukin-8) and MMP-2 (matrix metalloproteinase-2) secretion; and (iii) was still efficient during unglycosylated procathepsin L secretion. Thus down- or up-regulation of Rab4A expression or Rab4A function triggered inhibition or increase of procathepsin L secretion respectively. Furthermore, Rab4A regulation, by modifying procathepsin L secretion, switches the tumorigenic phenotype of human melanoma cells in nude mice.
Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding
Authors: Ghosh Abhrajyoti , Hartung Sophia , van der Does Chris , Tainer John A. , Albers Sonja-Verena
Published: June 2011

Microbial motility frequently depends on flagella or type IV pili. Using recently developed archaeal genetic tools, archaeal flagella and its assembly machinery have been identified. Archaeal flagella are functionally similar to bacterial flagella and their assembly systems are homologous with type IV pili assembly systems of Gram-negative bacteria. Therefore elucidating their biochemistry may result in insights in both archaea and bacteria. FlaI, a critical cytoplasmic component of the archaeal flagella assembly system in Sulfolobus acidocaldarius, is a member of the type II/IV secretion system ATPase superfamily, and is proposed to be bi-functional in driving flagella assembly and movement. In the present study we show that purified FlaI is a Mn2+-dependent ATPase that binds MANT-ATP [2′-/3′-O-(N′- methylanthraniloyl)adenosine-5′-O-triphosphate] with a high affinity and hydrolyses ATP in a co-operative manner. FlaI has an optimum pH and temperature of 6.5 and 75 °C for ATP hydrolysis. Remarkably, archaeal, but not bacterial, lipids stimulated the ATPase activity of FlaI 3–4-fold. Analytical gel filtration indicated that FlaI undergoes nucleotide-dependent oligomerization. Furthermore, SAXS (small-angle X-ray scattering) analysis revealed an ATP-dependent hexamerization of FlaI in solution. The results of the present study report the first detailed biochemical analyses of the motor protein of an archaeal flagellum.
Efficient numerical method for locating Feshbach resonances of ultracold molecules in external fields
Authors: Suleimanov Yury V. , Krems Roman V.
Published: June 2011

Collision properties of atoms and molecules in low temperature gases can be controlled by applying an external magnetic or electric field. The external field shifts the energy levels of the colliding particles, which gives rise to Feshbach resonances modifying the scattering cross sections. The resonances occur at particular magnitudes of the external field, where a bound state of the collision complex is degenerate with a scattering state. The positions of the resonances in the external field are usually identified by computing either the scattering cross sections or the bound states of the collision complex as functions of the external field magnitude. We propose a more efficient method for locating Feshbach resonances that requires neither of these computations. In particular, we show that the positions of Feshbach resonances can be identified by computing the log-derivative of the total wave function in a classically allowed region as a function of the external field strength. This procedure is particularly useful for locating narrow Feshbach resonances that may be hard to identify with the other methods.
Gaze Patterns during Identity and Emotion Judgments in Hearing Adults and Deaf Users of American Sign Language
Authors: Letourneau Susan M , Mitchell Teresa V
Published: June 2011

Deaf individuals rely on facial expressions for emotional, social, and linguistic cues. In order to test the hypothesis that specialized experience with faces can alter typically observed gaze patterns, twelve hearing adults and twelve deaf, early-users of American Sign Language judged the emotion and identity of expressive faces (including whole faces, and isolated top and bottom halves), while accuracy and fixations were recorded. Both groups recognized individuals more accurately from top than bottom halves, and emotional expressions from bottom than top halves. Hearing adults directed the majority of fixations to the top halves of faces in both tasks, but fixated the bottom half slightly more often when judging emotion than identity. In contrast, deaf adults often split fixations evenly between the top and bottom halves regardless of task demands. These results suggest that deaf adults have habitual fixation patterns that may maximize their ability to gather information from expressive faces.
Global standards and local knowledge building: Upgrading small producers in developing countries
Authors: Perez-Aleman Paola
Published: June 2011

Local knowledge building is a crucial factor for upgrading small producers and improving their market competitiveness and livelihoods. The rise of global standards affecting food safety and environmental sustainability in agriculture sparks debates on the impact on smallholders in developing countries. This article presents a perspective on the links of international standards to knowledge and institution building for developing the capabilities of small producers. Interacting with global practices, indigenous private and public actors create local institutions to develop capabilities for product and process innovations that contribute to economic development and enhance food security. Local innovation depends on collective strategic efforts through increasing networks among small producers and other organizations, including firms, nongovernmental organizations, and government, that foster knowledge circulation and bring diverse resources and support to build local capabilities.
Unconventional myristoylation of large-conductance Ca
2+
-activated K
+
channel (Slo1) via serine/threonine residues regulates channel surface expression
Authors: Alioua Abderrahmane , Li Min , Wu Yong , Stefani Enrico , Toro Ligia
Published: June 2011

Protein myristoylation is a means by which cells anchor proteins into membranes. The most common type of myristoylation occurs at an N-terminal glycine. However, myristoylation rarely occurs at an internal amino acid residue. Here we tested whether the α-subunit of the human large-conductance voltage- and Ca
2+
-activated K
+
channel (hSlo1) might undergo internal myristoylation. hSlo1 expressed in HEK293T cells incorporated [
3
H]myristic acid via a posttranslational mechanism, which is insensitive to cycloheximide, an inhibitor of protein biosynthesis. In-gel hydrolysis of [
3
H]myristoyl-hSlo1 with alkaline NH
2
OH (which cleaves hydroxyesters) but not neutral NH
2
OH (which cleaves thioesters) completely removed [
3
H]myristate from hSlo1, suggesting the involvement of a hydroxyester bond between hSlo1’s hydroxyl-bearing serine, threonine, and/or tyrosine residues and myristic acid; this type of esterification was further confirmed by its resistance to alkaline Tris·HCl. Treatment of cells expressing hSlo1 with 100 μM myristic acid caused alteration of hSlo1 activation kinetics and a 40% decrease in hSlo1 current density from 20 to 12 nA*MΩ. Immunocytochemistry confirmed a decrease in hSlo1 plasmalemma localization by myristic acid. Replacement of the six serines or the seven threonines (but not of the single tyrosine) of hSlo1 intracellular loops 1 and 3 with alanines decreased hSlo1 direct myristoylation by 40–44%, whereas in combination decreased myristoylation by nearly 90% and abolished the myristic acid-induced change in current density. Our data demonstrate that an ion channel, hSlo1, is internally and posttranslationally myristoylated. Myristoylation occurs mainly at hSlo1 intracellular loop 1 or 3, and is an additional mechanism for channel surface expression regulation.
Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species
Authors: Wani Revati , Qian Jiang , Yin Leimiao , Bechtold Erika , King S. Bruce , Poole Leslie B. , Paek Eunok , Tsang Allen W. , Furdui Cristina M.
Published: June 2011

Isoform-specific signaling of Akt, a major signaling hub and a prominent therapeutic target, remained poorly defined until recently. Subcellular distribution, tissue-specific expression, substrate specificity, and posttranslational modifications are believed to underlie isoform-specific signaling of Akt. The studies reported here show inhibition of Akt2 activity under physiologically relevant conditions of oxidation created by PDGF-induced reactive oxygen species. Combined MS and functional assays identified Cys124 located in the linker region between the N-terminal pleckstrin homology domain and the catalytic kinase domain as one of the unique regulatory redox sites in Akt2 with functional consequence on PDGF-stimulated glucose uptake. A model is proposed describing the consequence of increased endogenous oxidation induced by extracellular cues such as PDGF on Akt2 activity.
Polycystin-2 and phosphodiesterase 4C are components of a ciliary A-kinase anchoring protein complex that is disrupted in cystic kidney diseases
Authors: Choi Yun-Hee , Suzuki Akira , Hajarnis Sachin , Ma Zhendong , Chapin Hannah C. , Caplan Michael J. , Pontoglio Marco , Somlo Stefan , Igarashi Peter
Published: June 2011

Polycystic kidney disease (PKD) is a genetic disorder that is characterized by cyst formation in kidney tubules. PKD arises from abnormalities of the primary cilium, a sensory organelle located on the cell surface. Here, we show that the primary cilium of renal epithelial cells contains a protein complex comprising adenylyl cyclase 5/6 (AC5/6), A-kinase anchoring protein 150 (AKAP150), and protein kinase A. Loss of primary cilia caused by deletion of
Kif3a
results in activation of AC5 and increased cAMP levels. Polycystin-2 (PC2), a ciliary calcium channel that is mutated in human PKD, interacts with AC5/6 through its C terminus. Deletion of PC2 increases cAMP levels, which can be corrected by reexpression of wild-type PC2 but not by a mutant lacking calcium channel activity. Phosphodiesterase 4C (PDE4C), which catabolizes cAMP, is also located in renal primary cilia and interacts with the AKAP150 complex. Expression of PDE4C is regulated by the transcription factor hepatocyte nuclear factor-1β (HNF-1β), mutations of which produce kidney cysts. PDE4C is down-regulated and cAMP levels are increased in HNF-1β mutant kidney cells and mice. Collectively, these findings identify PC2 and PDE4C as unique components of an AKAP complex in primary cilia and reveal a common mechanism for dysregulation of cAMP signaling in cystic kidney diseases arising from different gene mutations.
Structural and functional characterization of an atypical activation domain in erythroid Krüppel-like factor (EKLF)
Authors: Mas Caroline , Lussier-Price Mathieu , Soni Shefali , Morse Thomas , Arseneault Geneviève , Di Lello Paola , Lafrance-Vanasse Julien , Bieker James J. , Omichinski James G.
Published: June 2011

Erythroid Krüppel-like factor (EKLF) plays an important role in erythroid development by stimulating β-globin gene expression. We have examined the details by which the minimal transactivation domain (TAD) of EKLF (EKLFTAD) interacts with several transcriptional regulatory factors. We report that EKLFTAD displays homology to the p53TAD and, like the p53TAD, can be divided into two functional subdomains (EKLFTAD1 and EKLFTAD2). Based on sequence analysis, we found that EKLFTAD2 is conserved in KLF2, KLF4, KLF5, and KLF15. In addition, we demonstrate that EKLFTAD2 binds the amino-terminal PH domain of the Tfb1/p62 subunit of TFIIH (Tfb1PH/p62PH) and four domains of CREB-binding protein/p300. The solution structure of the EKLFTAD2/Tfb1PH complex indicates that EKLFTAD2 binds Tfb1PH in an extended conformation, which is in contrast to the α-helical conformation seen for p53TAD2 in complex with Tfb1PH. These studies provide detailed mechanistic information into EKLFTAD functions as well as insights into potential interactions of the TADs of other KLF proteins. In addition, they suggest that not only have acidic TADs evolved so that they bind using different conformations on a common target, but that transitioning from a disordered to a more ordered state is not a requirement for their ability to bind multiple partners.
Galectin-9 binding to cell surface protein disulfide isomerase regulates the redox environment to enhance T-cell migration and HIV entry
Authors: Bi Shuguang , Hong Patrick W. , Lee Benhur , Baum Linda G.
Published: June 2011

Interaction of cell surface glycoproteins with endogenous lectins on the cell surface regulates formation and maintenance of plasma membrane domains, clusters signaling complexes, and controls the residency time of glycoproteins on the plasma membrane. Galectin-9 is a soluble, secreted lectin that binds to glycoprotein receptors to form galectin–glycoprotein lattices on the cell surface. Whereas galectin-9 binding to specific glycoprotein receptors induces death of CD4 Th1 cells, CD4 Th2 cells are resistant to galectin-9 death due to alternative glycosylation. On Th2 cells, galectin-9 binds cell surface protein disulfide isomerase (PDI), increasing retention of PDI on the cell surface and altering the redox status at the plasma membrane. Cell surface PDI regulates integrin function on platelets and also enhances susceptibility of T cells to infection with HIV. We find that galectin-9 binding to PDI on Th2 cells results in increased cell migration through extracellular matrix via β3 integrins, identifying a unique mechanism to regulate T-cell migration. In addition, galectin-9 binding to PDI on T cells potentiates infection with HIV. We identify a mechanism for regulating cell surface redox status via a galectin–glycoprotein lattice, to regulate distinct T-cell functions.
Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands
Authors: Das Payel , King Jonathan A. , Zhou Ruhong
Published: June 2011

The prevalent eye disease age-onset cataract is associated with aggregation of human γD-crystallins, one of the longest-lived proteins. Identification of the γ-crystallin precursors to aggregates is crucial for developing strategies to prevent and reverse cataract. Our microseconds of atomistic molecular dynamics simulations uncover the molecular structure of the experimentally detected aggregation-prone folding intermediate species of monomeric native γD-crystallin with a largely folded C-terminal domain and a mostly unfolded N-terminal domain. About 30 residues including a, b, and c strands from the Greek Key motif 4 of the C-terminal domain experience strong solvent exposure of hydrophobic residues as well as partial unstructuring upon N-terminal domain unfolding. Those strands comprise the domain–domain interface crucial for unusually high stability of γD-crystallin. We further simulate the intermolecular linkage of these monomeric aggregation precursors, which reveals domain-swapped dimeric structures. In the simulated dimeric structures, the N-terminal domain of one monomer is frequently found in contact with residues 135–164 encompassing the a, b, and c strands of the Greek Key motif 4 of the second molecule. The present results suggest that γD-crystallin may polymerize through successive domain swapping of those three C-terminal β-strands leading to age-onset cataract, as an evolutionary cost of its very high stability. Alanine substitutions of the hydrophobic residues in those aggregation-prone β-strands, such as L145 and M147, hinder domain swapping as a pathway toward dimerization. These findings thus provide critical molecular insights onto the initial stages of age-onset cataract, which is important for understanding protein aggregation diseases.
Pro-B cells sense productive immunoglobulin heavy chain rearrangement irrespective of polypeptide production
Authors: Lutz Johannes , Heideman Marinus R. , Roth Edith , van den Berk Paul , Müller Werner , Raman Chander , Wabl Matthias , Jacobs Heinz , Jäck Hans-Martin
Published: June 2011

B-lymphocyte development is dictated by the protein products of functionally rearranged Ig heavy (H) and light (L) chain genes. Ig rearrangement begins in pro-B cells at the IgH locus. If pro-B cells generate a productive allele, they assemble a pre-B cell receptor complex, which signals their differentiation into pre-B cells and their clonal expansion. Pre-B cell receptor signals are also thought to contribute to allelic exclusion by preventing further IgH rearrangements. Here we show in two independent mouse models that the accumulation of a stabilized μH mRNA that does not encode μH chain protein specifically impairs pro-B cell differentiation and reduces the frequency of rearranged IgH genes in a dose-dependent manner. Because noncoding IgH mRNA is usually rapidly degraded by the nonsense-mediated mRNA decay machinery, we propose that the difference in mRNA stability allows pro-B cells to distinguish between productive and nonproductive Ig gene rearrangements and that μH mRNA may thus contribute to efficient H chain allelic exclusion.
Perturbation of thymocyte development in nonsense-mediated decay (NMD)-deficient mice
Authors: Frischmeyer-Guerrerio Pamela A. , Montgomery Robert A. , Warren Daniel S. , Cooke Sara K. , Lutz Johannes , Sonnenday Christopher J. , Guerrerio Anthony L. , Dietz Harry C.
Published: June 2011

The random nature of T-cell receptor-β (TCR-β) recombination needed to generate immunological diversity dictates that two-thirds of alleles will be out-of-frame. Transcripts derived from nonproductive rearrangements are cleared by the nonsense-mediated mRNA decay (NMD) pathway, the process by which cells selectively degrade transcripts harboring premature termination codons. Here, we demonstrate that the fetal thymus in transgenic mice that ubiquitously express a dominant-negative form of Rent1/hUpf1, an essential
trans
-effector of NMD, shows decreased cell number, reduced CD4CD8 double-positive thymocytes, diminished expression of TCR-β, and increased expression of CD25, suggesting a defect in pre-TCR signaling. Transgenic fetal thymocytes also demonstrated diminished endogenous Vβ-to-DβJβ rearrangements, whereas Dβ-to-Jβ rearrangements were unperturbed, suggesting that inhibition of NMD induces premature shut-off of TCR-β rearrangement. Developmental arrest of thymocytes is prevented by the introduction of a fully rearranged TCR-β transgene that precludes generation of out-of-frame transcripts, suggesting direct mRNA-mediated
trans
-dominant effects. These data document that NMD has been functionally incorporated into developmental programs during eukaryotic evolution.
Lowering apolipoprotein CIII delays onset of type 1 diabetes
Authors: Holmberg Rebecka , Refai Essam , Höög Anders , Crooke Rosanne M. , Graham Mark , Olivecrona Gunilla , Berggren Per-Olof , Juntti-Berggren Lisa
Published: June 2011

Serum levels of apolipoprotein CIII (apoCIII) are increased in type 1 diabetic patients, and when β cells are exposed to these diabetic sera, apoptosis occurs, an effect abolished by an antibody against apoCIII. We have investigated the BB rat, an animal model that develops a human-like type 1 diabetes, and found that apoCIII was also increased in sera from prediabetic rats. This increase in apoCIII promoted β-cell death. The endogenous levels of apoCIII were reduced by treating prediabetic animals with an antisense against this apolipoprotein, resulting in a significantly delayed onset of diabetes. ApoCIII thus serves as a diabetogenic factor, and intervention with this apolipoprotein in the prediabetic state can arrest disease progression. These findings suggest apoCIII as a target for the treatment of type 1 diabetes.
HLA-E expression by gynecological cancers restrains tumor-infiltrating CD8+T lymphocytes
Authors: Gooden Marloes , Lampen Margit , Jordanova Ekaterina S. , Leffers Ninke , Trimbos J. Baptist , van der Burg Sjoerd H. , Nijman Hans , van Hall Thorbald
Published: June 2011

HLA-E is a nonclassical HLA class I molecule, which differs from classical HLA molecules by its nonpolymorphic, conserved nature. Expression and function of HLA-E in normal tissues and solid tumors is not fully understood. We investigated HLA-E protein expression on tissue sections of 420 ovarian and cervical cancers and found equal or higher levels than normal counterpart epithelia in 80% of the tumors. Expression was strongly associated with components of the antigen presentation pathway, e.g., transporter associated with antigen processing (TAP), endoplasmic reticulum aminopeptide (ERAP), β2 microglobulin (β2m), HLA classes I and II, and for ovarian cancer with tumor infiltrating CD8+T lymphocytes (CTLs). This association argues against the idea that HLA-E would compensate for the loss of classical HLA in tumors. In situ detection of HLA-E interacting receptors revealed a very low infiltrate of natural killer (NK) cells, but up to 50% of intraepithelial CTLs expressed the inhibiting CD94/NKG2A receptor. In cervical cancer, HLA-E expression did not alter the prognostic effect of CTLs, most likely due to very high infiltrating CTL numbers in this virus-induced tumor. Overall survival of ovarian cancer patients, however, was strongly influenced by HLA-E, because the beneficial effect of high CTL infiltration was completely neutralized in the subpopulation with strong HLA-E expression. Interestingly, these results indicate that CTL infiltration in ovarian cancer is associated with better survival only when HLA-E expression is low and that intratumoral CTLs are inhibited by CD94/NKG2A receptors on CTLs in the tumor microenvironment.
Replication and segregation of an
Escherichia coli
chromosome with two replication origins
Authors: Wang Xindan , Lesterlin Christian , Reyes-Lamothe Rodrigo , Ball Graeme , Sherratt David J.
Published: June 2011

Characterized bacteria, unlike eukaryotes and some archaea, initiate replication bidirectionally from a single replication origin contained within a circular or linear chromosome. We constructed
Escherichia coli
cells with two WT origins separated by 1 Mb in their 4.64-Mb chromosome. Productive bidirectional replication initiated synchronously at both spatially separate origins. Newly replicated DNA from both origins was segregated sequentially as replication progressed, with two temporally and spatially separate replication termination events. Replication initiation occurred at a cell volume identical to that of cells with a single WT origin, showing that initiation control is independent of cellular and chromosomal
oriC
concentration. Cells containing just the ectopic origin initiated bidirectional replication at the expected cell mass and at the normal cellular location of that region. In all strains, spatial separation of sister loci adjacent to active origins occurred shortly after their replication, independently of whether replication initiated at the normal origin, the ectopic origin, or both origins.
B regulatory cells and the tumor-promoting actions of TNF-α during squamous carcinogenesis
Authors: Schioppa Tiziana , Moore Robert , Thompson Richard G. , Rosser Elizabeth C. , Kulbe Hagen , Nedospasov Sergei , Mauri Claudia , Coussens Lisa M. , Balkwill Frances R.
Published: June 2011

The inflammatory cytokine TNF-α has been recognized as a critical tumor promoter, but the effector cells that mediate its action have not been fully characterized. Because B cells regulate squamous and prostate carcinogenesis, andTnf−/−mice harbor B-cell defects, we investigated the hypothesis that B cells are important effector cells for TNF-α–mediated promotion of cancer development. Using an adoptive transfer strategy and the 7,12-dimethylbenz[α]anthracene/terephthalic acid (DMBA/TPA) two-stage model of skin carcinogenesis, we found that both B cells and TNF-α are critical for the development of DMBA/TPA-induced papilloma. Transfer of B cells from DMBA/TPA-treated wild-type mice toTnf−/−mice rescued papilloma development to a wild-type level, a result not observed when B cells fromTnf−/−mice were transferred toRag2−/−mice or when TNF-α was eliminated selectively in B cells. Resistance to papilloma development inTnf−/−mice was associated with increased IFN-γ and CD8+T cells in skin and a significant reduction in IL-10–producing B regulatory cells alongside an increase in IFN-γ–producing CD8+T cells in the spleen. These data indicate that during DMBA/TPA-induced squamous carcinogenesis TNF-α mediates tumor-promoting activity via regulatory B cells that repress antitumor immunity.
The
Legionella
HtrA homologue DegQ is a self-compartmentizing protease that forms large 12-meric assemblies
Authors: Wrase Robert , Scott Hannah , Hilgenfeld Rolf , Hansen Guido
Published: June 2011

Proteases of the HtrA family are key factors dealing with folding stress in the periplasmatic compartment of prokaryotes. In
Escherichia coli
, the well-characterized HtrA family members DegS and DegP counteract the accumulation of unfolded outer-membrane proteins under stress conditions. Whereas DegS serves as a folding-stress sensor, DegP is a chaperone-protease facilitating refolding or degradation of defective outer-membrane proteins. Here, we report the 2.15-Å-resolution crystal structure of the second major chaperone-protease of the periplasm, DegQ from
Legionella fallonii
. DegQ assembles into large, cage-like 12-mers that form independently of unfolded substrate proteins. We provide evidence that 12-mer formation is essential for the degradation of substrate proteins but not for the chaperone activity of DegQ. In the current model for the regulation of periplasmatic chaperone-proteases, 6-meric assemblies represent important protease-resting states. However, DegQ is unable to form such 6-mers, suggesting divergent regulatory mechanisms for DegQ and DegP. To understand how the protease activity of DegQ is controlled, we probed its functional properties employing designed protein variants. Combining crystallographic, biochemical, and mutagenic data, we present a mechanistic model that suggests how protease activity of DegQ 12-mers is intrinsically regulated and how deleterious proteolysis by free DegQ 3-mers is prevented. Our study sheds light on a previously uncharacterized component of the prokaryotic stress-response system with implications for other members of the HtrA family.
An antigenic peptide produced by reverse splicing and double asparagine deamidation
Authors: Dalet Alexandre , Robbins Paul F. , Stroobant Vincent , Vigneron Nathalie , Li Yong F. , El-Gamil Mona , Hanada Ken-ichi , Yang James C. , Rosenberg Steven A. , Van den Eynde Benoît J.
Published: June 2011

A variety of unconventional translational and posttranslational mechanisms contribute to the production of antigenic peptides, thereby increasing the diversity of the peptide repertoire presented by MHC class I molecules. Here, we describe a class I-restricted peptide that combines several posttranslational modifications. It is derived from tyrosinase and recognized by tumor-infiltrating lymphocytes isolated from a melanoma patient. This unusual antigenic peptide is made of two noncontiguous tyrosinase fragments that are spliced together in the reverse order. In addition, it contains two aspartate residues that replace the asparagines encoded in the tyrosinase sequence. We confirmed that this peptide is naturally presented at the surface of melanoma cells, and we showed that its processing sequentially requires translation of tyrosinase into the endoplasmic reticulum and its retrotranslocation into the cytosol, where deglycosylation of the two asparagines by peptide-N-glycanase turns them into aspartates by deamidation. This process is followed by cleavage and splicing of the appropriate fragments by the standard proteasome and additional transport of the resulting peptide into the endoplasmic reticulum through the transporter associated with antigen processing (TAP).
Differential curvature sensing and generating activities of dynamin isoforms provide opportunities for tissue-specific regulation
Authors: Liu Ya-Wen , Neumann Sylvia , Ramachandran Rajesh , Ferguson Shawn M. , Pucadyil Thomas J. , Schmid Sandra L.
Published: June 2011

Dynamin 1 (Dyn1) and Dyn2 are neuronal and ubiquitously expressed isoforms, respectively, of the multidomain GTPase required for clathrin-mediated endocytosis (CME). Although they are 79% identical, Dyn1 and Dyn2 are not fully functionally redundant. Through direct measurements of basal and assembly-stimulated GTPase activities, membrane binding, self-assembly, and membrane fission on planar and curved templates, we have shown that Dyn1 is an efficient curvature generator, whereas Dyn2 is primarily a curvature sensor. Using Dyn1/Dyn2 chimeras, we identified the lipid-binding pleckstrin homology domain as being responsible for the differential in vitro properties of these two isoforms. Remarkably, their in vitro activities were reversed by a single amino acid change in the membrane-binding variable loop 3. Reconstitution of KO mouse embryo fibroblasts showed that both the pleckstrin homology and the Pro/Arg-rich domains determine the differential abilities of these two isoforms to support CME. These domains are specific to classical dynamins and are involved in regulating their activity. Our findings reveal opportunities for fundamental differences in the regulation of Dyn1, which mediates rapid endocytosis at the synapse, vs. Dyn2, which regulates early and late events in CME in nonneuronal cells.
Effector-triggered immunity blocks pathogen degradation of an immunity-associated vesicle traffic regulator in
Arabidopsis
Authors: Nomura Kinya , Mecey Christy , Lee Young-Nam , Imboden Lori Alice , Chang Jeff H. , He Sheng Yang
Published: June 2011

Innate immunity in plants can be triggered by microbe- and pathogen-associated molecular patterns. The pathogen-associated molecular pattern-triggered immunity (PTI) is often suppressed by pathogen effectors delivered into the host cell. Plants can overcome pathogen suppression of PTI and reestablish pathogen resistance through effector-triggered immunity (ETI). An unanswered question is how plants might overcome pathogen-suppression of PTI during ETI. Findings described in this paper suggest a possible mechanism. During
Pseudomonas syringae
pathovar
tomato
(
Pst
) DC3000 infection of
Arabidopsis
, a host ADP ribosylation factor guanine nucleotide exchange factor, AtMIN7, is destabilized by the pathogen effector HopM1 through the host 26S proteasome. In this study, we discovered that AtMIN7 is required for not only PTI, consistent with the notion that
Pst
DC3000 degrades AtMIN7 to suppress PTI, but also ETI. The AtMIN7 level in healthy plants is low, but increases posttranscriptionally in response to activation of PTI. Whereas DC3000 infection led to degradation of AtMIN7, activation of ETI by three different effectors, AvrRpt2, AvrPphB, and HopA1, in Col-0 plants blocks the ability of
Pst
DC3000 to destabilize AtMIN7. Further analyses of bacterial translocation of HopM1 and AtMIN7 stability in HopM1 transgenic plants show that ETI prevents HopM1-mediated degradation of AtMIN7 inside the plant cell. Both AtMIN7 and HopM1 are localized to the
trans
-Golgi network/early endosome, a subcellular compartment that is not previously known to be associated with bacterial pathogenesis in plants. Thus, blocking pathogen degradation of
trans
-Golgi network/early endosome-associated AtMIN7 is a critical part of the ETI mechanism to counter bacterial suppression of PTI.
Role of antibiotic ligand in nascent peptide-dependent ribosome stalling
Authors: Vázquez-Laslop Nora , Klepacki Dorota , Mulhearn Debbie C. , Ramu Haripriya , Krasnykh Olga , Franzblau Scott , Mankin Alexander S.
Published: June 2011

Specific nascent peptides in the ribosome exit tunnel can elicit translation arrest. Such ribosome stalling is used for regulation of expression of some bacterial and eukaryotic genes. The stalling is sensitive to additional cellular cues, most commonly the binding of specific small-molecular-weight cofactors to the ribosome. The role of cofactors in programmed translation arrest is unknown. By analyzing nascent peptide- and antibiotic-dependent ribosome stalling that controls inducible expression of antibiotic resistance genes in bacteria, we have found that the antibiotic is directly recognized as a part of the translation modulating signal. Even minute structural alterations preclude it from assisting in ribosome stalling, indicating the importance of precise molecular interactions of the drug with the ribosome. One of the sensors that monitor the structure of the antibiotic is the 23S rRNA residue C2610, whose mutation reduces the efficiency of nascent peptide- and antibiotic-dependent ribosome stalling. These findings establish a new paradigm of the role of the cofactor in programmed translation arrest in which a small molecule is recognized along with specific nascent peptide sequences as a composite structure that provokes arrest of translation. A similar mechanism could be used by the ribosome to sense a variety of cellular metabolites.
Unique scorpion toxin with a putative ancestral fold provides insight into evolution of the inhibitor cystine knot motif
Authors: Smith Jennifer J. , Hill Justine M. , Little Michelle J. , Nicholson Graham M. , King Glenn F. , Alewood Paul F.
Published: June 2011

The three-disulfide inhibitor cystine knot (ICK) motif is a fold common to venom peptides from spiders, scorpions, and aquatic cone snails. Over a decade ago it was proposed that the ICK motif is an elaboration of an ancestral two-disulfide fold coined the disulfide-directed β-hairpin (DDH). Here we report the isolation, characterization, and structure of a novel toxin [U
1
-liotoxin-Lw1a (U
1
-LITX-Lw1a)] from the venom of the scorpion
Liocheles waigiensis
that is the first example of a native peptide that adopts the DDH fold. U
1
-LITX-Lw1a not only represents the discovery of a missing link in venom protein evolution, it is the first member of a fourth structural fold to be adopted by scorpion-venom peptides. Additionally, we show that U
1
-LITX-Lw1a has potent insecticidal activity across a broad range of insect pest species, thereby providing a unique structural scaffold for bioinsecticide development.
Direct visualization at the single-cell level of siRNA electrotransfer into cancer cells
Authors: Paganin-Gioanni A. , Bellard E. , Escoffre J. M. , Rols M. P. , Teissié J. , Golzio M.
Published: June 2011

The RNA interference-mediated gene silencing approach is promising for therapies based on the targeted inhibition of disease-relevant genes. Electropermeabilization is one of the nonviral methods successfully used to transfer siRNA into living cells in vitro and in vivo. Although this approach is effective in the field of gene silencing by RNA interference, very little is known about the basic processes supporting siRNA transfer. In this study, we investigated, by direct visualization at the single-cell level, the delivery of Alexa Fluor 546-labeled siRNA into murine melanoma cells stably expressing the enhanced green fluorescent protein (EGFP) as a target gene. The electrotransfer of siRNA was quantified by time lapse fluorescence microscopy and was correlated with the silencing of
egfp
expression. A direct transfer into the cell cytoplasm of the negatively charged siRNA was observed across the plasma membrane exclusively on the side facing the cathode. When added after electropulsation, the siRNA was inefficient for gene silencing because it did not penetrate the cells. Therefore, we report that an electric field acts on both the permeabilization of the cell plasma membrane and on the electrophoretic drag of the negatively charged siRNA molecules from the bulk phase into the cytoplasm. The transfer kinetics of siRNA are compatible with the creation of nanopores, which are described with the technique of synthetic nanopores. The mechanism involved was clearly specific for the physico-chemical properties of the electrotransferred molecule and was different from that observed with small molecules or plasmid DNA.