Published by De Gruyter

Volume 391 Issue 2-3

Issue of Biological Chemistry

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Contents
Journal Overview

EDITORIAL

March 4, 2010

Highlight: Signal Transduction and Disease

Fred Wittinghofer

Page range: 129-129

Abstract

No abstract available

HIGHLIGHT: SIGNAL TRANSDUCTION AND DISEASE

February 26, 2010

Phosphorylase and the origin of reversible protein phosphorylation

Edmond H. Fischer

Page range: 131-137

Abstract

This article presents a historical account of the discovery of reversible protein phosphorylation. The process was uncovered in the mid-1950s in a study designed to elucidate the complex hormonal regulation of skeletal muscle glycogen phosphorylase. This enzyme was originally thought to be regulated by AMP now known to serve as an allosteric effector. By contrast, hormonal regulation was found to result from a phosphorylation of the protein triggered by Ca 2+ and ATP which activate phosphorylase kinase; the reverse reaction is catalyzed by a phosphorylase phosphatase. Although that reaction is extremely simple, it came nevertheless as a complete surprise because essentially nothing was known at that time about the structure and function of phosphoproteins. This study led to the establishment of the first hormonal cascade of successive enzymatic reactions, kinases acting on kinases, initiated by cAMP discovered by Earl Sutherland. It also showed how two different physiological processes (carbohydrate metabolism and muscle contraction) could be regulated in concert. The regulation of phosphorylase was so straightforward that it was thought to represent the prototype for these kinds of interconversions. We know today that it was almost the absolute exception.

February 26, 2010

β-Catenin as a multilayer modulator of zonal cytochrome P450 expression in mouse liver

Albert Braeuning, Michael Schwarz

Page range: 139-148

Abstract

The liver is the major organ for metabolism of drugs and other xenobiotics. Expression of many drug-metabolizing enzymes is not equally distributed throughout the liver: under normal conditions, many of them, including the most relevant members of the cytochrome P450 superfamily, are exclusively expressed in a hepatocyte subpopulation located near branches of the efferent central vein. Activation of different ligand-dependent transcription factors by exogenous compounds stimulates high expression of certain cytochrome P450 isoforms. This process also occurs preferentially in perivenous hepatocytes. The mechanisms, however, which determine the zone-specificity of basal and xenobiotic-induced expression of cytochrome P450 enzymes, have remained largely unknown for decades. Very recently, signaling through the Wnt/β-catenin pathway has been implicated in the regulation of zonal gene expression in mouse liver. In this review, current knowledge of cytochrome P450 regulation by β-catenin-dependent transcription is summarized and underlying molecular mechanisms are discussed.

February 3, 2010

Glycome profiling using modern glycomics technology: technical aspects and applications

Dieter Vanderschaeghe, Nele Festjens, Joris Delanghe, Nico Callewaert

Page range: 149-161

Abstract

Glycomics research has become indispensable in many research fields such as immunity, signal transduction and development. Moreover, changes in the glycosylation of proteins and lipids have been reported in several diseases including cancer. The analysis of a complex post-translational modification such as glycosylation depends on the availability or development of appropriate analytical technologies. The research goal determines the sensitivity, resolution and throughput requirements and guides the choice of a particular technology. This review highlights the evolution of glycan profiling tools in the past 5 years. We focus on capillary electrophoresis, liquid chromatography, mass spectrometry and lectin microarrays.

February 26, 2010

Ubiquitin ligase complexes: from substrate selectivity to conjugational specificity

Vanja Nagy, Ivan Dikic

Page range: 163-169

Abstract

Localization, activity and lifespan of a protein are signaled by a small, 8 kDa protein, ubiquitin (Ub). Ub conjugation is a post-translational modification orchestrated by the sequential action of activating (E1), conjugating (E2), and ligating (E3) enzymes. Although a simple combination of an E2 and an E3 enzyme can be sufficient for an active complex, in other cases ubiquitination can occur in the context of large multimeric complexes with enhanced molecular abilities. Here, we review several Ub ligase complexes to highlight strategies governing conjugational specificity, the gained adaptability in substrate specificity, and modulatory flexibility encoded in regulatory components of these diverse multimers.

February 3, 2010

MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway

Ser Sue Ng, Tokameh Mahmoudi, Vivian S.W. Li, Pantelis Hatzis, Paul J. Boersema, Shabaz Mohammed, Albert J. Heck, Hans Clevers

Page range: 171-180

Abstract

A central point of regulation in the Wnt/β-catenin signalling pathway is the formation of the β-catenin destruction complex. Axin1, an essential negative regulator of Wnt signalling, serves as a scaffold within this complex and is critical for rapid turnover of β-catenin. To examine the mechanism by which Wnt signalling disables the destruction complex, we used an immunoprecipitation-coupled proteomics approach to identify novel endogenous binding partners of Axin1. We found mitogen-activated protein kinase kinase kinase 1 (MAP3K1) as an Axin1 interactor in Ls174T colorectal cancer (CRC) cells. Importantly, confirmation of this interaction in HEK293T cells indicated that the Axin1-MAP3K1 interaction is induced and modulated by Wnt stimulation. siRNA depletion of MAP3K1 specifically abrogated TCF/LEF-driven transcription and Wnt3A-driven endogenous gene expression in both HEK293T as well as DLD-1 CRC. Expression of ubiquitin ligase mutants of MAP3K1 abrogated TCF/LEF transcription, whereas kinase mutants had no effect in TCF-driven activity, highlighting the essential role of the MAP3K1 E3 ubiquitin ligase activity in regulation of the Wnt/β-catenin pathway. These results suggest that MAP3K1, previously reported as an Axin1 inter-actor in c-Jun NH 2 -terminal kinase pathway, is also involved in the canonical Wnt signalling pathway and positively regulates expression of Wnt target genes.

February 3, 2010

Signal transduction by the atopy-associated human thymic stromal lymphopoietin (TSLP) receptor depends on Janus kinase function

Andreas Wohlmann, Katrin Sebastian, Andreas Borowski, Sebastian Krause, Karlheinz Friedrich

Page range: 181-186

Abstract

Thymic stromal lymphopoietin (TSLP) is an interleukin-(IL)-7-like cytokine with emerging pathological importance for the development of atopic diseases such as allergic asthma bronchiale. The TSLP receptor (TSLPR), a heterodimeric type I cytokine receptor, shares the IL-7R α-subunit with the IL-7 receptor system. The specific TSLPR α-chain shows similarities with the γc receptor chain, but has some unusual features within the receptor family in both its ligand-binding and cytoplasmic domain. The murine TSLPR signals via the signal transducers and activators of transcription STAT5 and STAT3, but is unique among cytokine receptors in that it activates STATs without the involvement of Janus (JAK) tyrosine kinases, but instead utilizes the Src type kinase Tec. Here, we show by Western blotting and reporter gene experiments in combination with the application of a specific JAK inhibitor that the human TSLP receptor, in contrast, requires the function of JAK1 and JAK2 for STAT activation. Moreover, we demonstrate that the human TSLPR mediates gene regulation not only through STAT5 and STAT3 but has also the potential to mediate transcription via STAT1. Our work should help to understand more thoroughly how TSLP triggers inflammatory responses in the course of atopic diseases.

GENES AND NUCLEIC ACIDS

February 26, 2010

6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products

Reinhild Wurm, Thomas Neußer, Rolf Wagner

Page range: 187-196

Abstract

6S RNA from Escherichia coli is known to bind to RNA polymerase, preventing interaction with many promoters during stationary growth. The resulting repression is released under conditions of nutritional upshift, when the growth situation improves. 6S RNA, which binds to the active site of RNA polymerase, has the particularly interesting feature to act as a template, causing the transcription of defined de novo RNAs (dnRNA) that are complementary to a specific sequence region of the 6S RNA. We analyzed the conditions of dnRNA synthesis and determined their effect on the 6S RNA-mediated inhibition of RNA polymerase in vitro and in vivo . Upon nutritional upshift the RNA polymerase/6S RNA complex induces the rapid synthesis of dnRNAs, which form stable hybrids with the 6S RNA template. The resulting structural change destabilizes the inactivated RNA polymerase complex, causing σ subunit release. Both dnRNA and 6S RNA are rapidly degraded after complex disintegration. Experiments using the transcriptional inhibitor rifampicin demonstrate that active transcription is required for the disintegration of the RNA polymerase/6S RNA complex. Our results support the conclusion that 6S RNA not only inhibits transcription during stationary growth but also enables cells to resume rapid growth after starvation and help to escape from stationary phase.

PROTEIN STRUCTURE AND FUNCTION

February 3, 2010

Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation

Jitka Malcikova, Boris Tichy, Jiri Damborsky, Jitka Kabathova, Martin Trbusek, Jiri Mayer, Sarka Pospisilova

Page range: 197-205

Abstract

Sequence-specific DNA binding is the key function through which tumor suppressor p53 exerts transactivation of the downstream target genes, often being impaired in cancer cells by mutations in the TP53 gene. Functional protein microarray technology enables a high-throughput parallel analysis of protein properties within one experiment under the same conditions. Using an array approach, we analyzed the DNA binding activity of wild type p53 protein and of 49 variants. Our results show significant differences in the binding properties between the p53 mutants. The C-terminal mutant R337C displayed the highest DNA binding activity on the array. However, the same mutant showed only a partial activation in the reporter gene assay and almost no activation of downstream target genes after transfection of expression vector into cells lacking endogenous p53. These observations demonstrate that DNA binding itself is not sufficient for activating the p53 target genes in at least some of the p53 mutants and, therefore, in vitro studies might not always reflect in vivo conditions.

February 26, 2010

Peptides from the Mycobacterium tuberculosis Rv1980c protein involved in human cell infection: insights into new synthetic subunit vaccine candidates

Diana Rodríguez, Carolina Vizcaíno, Marisol Ocampo, Hernando Curtidor, Marta Pinto, Manuel Elkin Patarroyo, Manuel Alfonso Patarroyo

Page range: 207-217

Abstract

Mycobacterium tuberculosis infection continues to be a major cause of morbidity and mortality throughout the world. The vast complexity of the intracellular pathogen M. tuberculosis and the diverse mechanisms by which it can invade host cells highlight the importance of developing a fully protective vaccine. Our vaccine development strategy consists of including fragments from multiple mycobacterial proteins involved in cell invasion. The aim of this study was to identify high activity binding peptides (HABPs) in the immunogenic protein Rv1980c from M. tuberculosis H37Rv with the ability to inhibit mycobacterial invasion into U937 monocyte-derived macrophages and A549 cells. The presence and transcription of the Rv1980c gene was assessed in members belonging to the M. tuberculosis complex and other nontuberculous mycobacteria by PCR and RT-PCR, respectively. Cell surface localization was confirmed by immuno-electron microscopy. Three peptides binding with high activity to U937 cells and one to A549 cells were identified. HABPs 31100, 31101, and 31107 inhibited invasion of M. tuberculosis into A549 and U937 cells and therefore could be promising candidates for the design of a subunit-based antituberculous vaccine.

February 26, 2010

The epimerase activity of anthocyanidin reductase from Vitis vinifera and its regiospecific hydride transfers

Mahmoud Gargouri, Jean Chaudière, Claude Manigand, Chloé Maugé, Katell Bathany, Jean-Marie Schmitter, Bernard Gallois

Page range: 219-227

Abstract

Anthocyanidin reductase (ANR) from Vitis vinifera catalyzes an NADPH-dependent double reduction of anthocyanidins producing a mixture of (2S,3R)- and (2S,3S)-flavan-3-ols. At pH 7.5 and 30°C, the first hydride transfer to anthocyanidin is irreversible, and no intermediate is released during catalysis. ANR reverse activity was assessed in the presence of excess NADP + . Analysis of products by reverse phase and chiral phase HPLC demonstrates that ANR acts as a flavan-3-ol C 3 -epimerase under such conditions, but this is only observed with 2R-flavan-3-ols, not with 2S-flavan-3-ols produced by the enzyme in the forward reaction. In the presence of deuterated coenzyme 4S-NADPD, ANR transforms anthocyanidins into dideuterated flavan-3-ols. The regiospecificity of deuterium incorporation into catechin and afzelechin – derived from cyanidin and pelargonidin, respectively – was analyzed by liquid chromatography coupled with electro- spray ionization-tandem mass spectrometry (LC/ESI-MS/MS), and it was found that deuterium was always incorporated at C 2 and C 4 . We conclude that C 3 -epimerization should be achieved by tautomerization between the two hydride transfers and that this produces a quinone methide intermediate which serves as C 4 target of the second hydride transfer, thereby avoiding any stereospecific modification of carbon 3. The inversion of C 2 stereochemistry required for ‘reverse epimerization’ suggests that the 2S configuration induces an irreversible product dissociation.

February 26, 2010

Antibacterial activity of radical scavengers against class Ib ribonucleotide reductase from Bacillus anthracis

Eduard Torrents, Britt-Marie Sjöberg

Page range: 229-234

Abstract

Bacillus anthracis is a severe mammalian pathogen. The deoxyribonucleotides necessary for DNA replication and repair are provided via the ribonucleotide reductase (RNR) enzyme. RNR is also important for spore germination and cell proliferation upon infection. We show that the expression of B. anthracis class Ib RNR responds to the environment that the pathogen encounters upon infection. We also show that several anti-proliferative agents (radical scavengers) specifically inhibit the B. anthracis RNR. Owing to the importance of RNR in the pathogenic infection process, our results highlight a promising potential to inhibit the growth of B. anthracis early during infection.

CELL BIOLOGY AND SIGNALING

February 26, 2010

Signal transduction in CHO cells stably transfected with domain-selective forms of murine ACE

Xiaoou Sun, Brit Rentzsch, Maolian Gong, Jenny Eichhorst, Kristin Pankow, Gisela Papsdorf, Björn Maul, Michael Bader, Wolf-Eberhard Siems

Page range: 235-244

Abstract

Membrane-bound human angiotensin-converting enzyme (ACE) has been reported to initiate intracellular signaling after interaction with substrates or inhibitors. Somatic ACE is known to contain two distinct, extracellular catalytic centers. We analyzed the signal transduction mechanisms in cells transfected with different forms of murine ACE (mACE) and investigated whether the two domains are similarly involved in these processes. For this purpose, CHO cells were stably transfected with mACE or with its domain-selective mutants. In addition to these modified cellular models, human umbilical vein endothelial cells were used in this study. Signal transduction molecules such as JNK and c-Jun were analyzed after activation of cells with several ACE substrates and inhibitors. ACE-targeting compounds such as substrates, inhibitors, or even the ACE product angiotensin-II induce in mACE-expressing cells a signal transduction response. These processes are also evoked by partially inactivated forms of mACE and finally result in an enhanced cyclooxygenase-2 transcription. Surprisingly, the membrane-bound ACE activity is also influenced by ACE-targeted interventions. Our data suggest that the two catalytic domains of mACE do not function independently but that the signal transduction is influenced by negative cooperativity of the two catalytic domains. This study underlines that ACE indeed has receptor-like properties which occur in a species-specific manner.

February 26, 2010

The impact of methylmercury on 1,25-dihydroxyvitamin D3-induced transcriptomic responses in dolphin skin cells

Blake C. Ellis, Sebastiano Gattoni-Celli, Mark S. Kindy

Page range: 245-258

Abstract

The Atlantic bottlenose dolphin has been the focus of much attention owing to the considerable impact of environmental stress on its health and the associated implications for human health. Here, we used skin cells from the dolphin to investigate the protective role of the vitamin D pathway against environmental stressors. We previously reported that dolphin skin cells respond to 1,25-dihydroxyvitamin D3 (1,25D3), the bioactive metabolite of vitamin D3, by upregulation of the vitamin D receptor (VDR) and expression of several genes. Methylmercury is a highly bioaccumulative environmental stressor of relevance to the dolphin. We currently report that in dolphin cells sublethal concentrations of methylmercury compromise the ability of 1,25D3 to upregulate VDR, to transactivate a vitamin D-sensitive promoter, and to express specific target genes. These results help elucidate the effects of vitamin D and methylmercury on innate immunity in dolphin skin and potentially in human skin as well, considering similarities in the vitamin D pathway between the two species.

PROTEOLYSIS

February 26, 2010

An examination of the proteolytic activity for bovine pregnancy-associated glycoproteins 2 and 12

Bhanu Prakash V.L. Telugu, Mark O. Palmier, Steven R. Van Doren, Jonathan A. Green

Page range: 259-270

Abstract

The pregnancy-associated glycoproteins (PAGs) represent a complex group of putative aspartic peptidases expressed exclusively in the placentas of species in the Artiodactyla order. The ruminant PAGs segregate into two classes: the ‘ancient’ and ‘modern’ PAGs. Some of the modern PAGs possess alterations in the catalytic center that are predicted to preclude their ability to act as peptidases. The ancient ruminant PAGs in contrast are thought to be peptidases, although no proteolytic activity has been described for these members. The aim of the present study was to investigate (1) if the ancient bovine PAGs (PAG-2 and PAG-12) have proteolytic activity, and (2) if there are any differences in activity between these two closely related members. Recombinant bovine PAG-2 and PAG-12 were expressed in a baculovirus expression system and the purified proteins were analyzed for proteolytic activity against a synthetic fluorescent cathepsin D/E substrate. Both proteins exhibited proteolytic activity with acidic pH optima. The k cat / K m for bovine PAG-2 was 2.7×10 5 m -1 s -1 and for boPAG-12 it was 6.8×10 4 m -1 s -1 . The enzymes were inhibited by pepstatin A with a K i of 0.56 and 7.5 n m for boPAG-2 and boPAG-12, respectively. This is the first report describing proteolytic activity in PAGs from ruminant ungulates.

February 26, 2010

Analysis of an autoproteolytic activity of rice yellow mottle virus silencing suppressor P1

Isabel Weinheimer, Kajohn Boonrod, Mirko Moser, Michèle Zwiebel, Marc Füllgrabe, Gabi Krczal, Michael Wassenegger

Page range: 271-281

Abstract

Ectopically expressed rice yellow mottle virus P1 fusion proteins were found to be cleaved in planta and in Escherichia coli . Cleavage takes place in the absence of bacterial protease activity, indicating that the P1 fusion is autocatalytically processed independently of host factors. N-terminal sequencing of the C-terminal cleavage product of transiently expressed P1/GFP (green fluorescence protein) in Nicotiana benthamiana showed that the cleavage site is located between the first two amino acids (aa) downstream of the P1 sequence. Mutagenesis experiments revealed that a phenylalanine to valine substitution at position 157 of the P1 aa sequence impairs proper cleavage, which is nearly unaffected by replacement of phenylalanine with tyrosine. Deletion of methionine 159 (first GFP aa residue) appeared to not affect P1/GFP cleavage. N-terminal P1-tagging with GFP turned out to impair autocleavage, whereas a small His-tag could not fully prevent cleavage. Additionally, a modified P1/GFP carrying an N-terminal deletion of 81 aa was not cleaved. These findings indicate that this region is involved in the proteolysis mechanism and that large N-terminal fusion partners might affect correct folding of the P1 necessary for self-catalysis.

February 3, 2010

Identification of novel peptide inhibitors for human trypsins

Ping Wu, Janne Weisell, Miikka Pakkala, Mikael Peräkylä, Lei Zhu, Riitta Koistinen, Erkki Koivunen, Ulf-Håkan Stenman, Ale Närvänen, Hannu Koistinen

Page range: 283-293

Abstract

Human trypsin isoenzymes share extensive sequence similarity, but certain differences in their activity and susceptibility to inhibitors have been observed. Using phage display technology, we identified seven different peptides that bind to and inhibit the activity of trypsin-3, a minor trypsin isoform expressed in pancreas and brain. All of the peptides contain at least two of the amino acids tryptophan, alanine and arginine, whereas proline was found closer to the N-terminus in all but one peptide. All peptides contain two or more cysteines, suggesting a cyclic structure. However, we were able to make synthetic linear variants of these peptides without losing bioactivity. Alanine replacement experiments for one of the peptides suggest that the IPXXWFR motif is important for activity. By molecular modeling the same amino acids were found to interact with trypsin-3. The peptides also inhibit trypsin-1, but only weakly, if at all, trypsin-2 and -C. As trypsin is a highly active enzyme which can activate protease-activated receptors and enzymes that participate in proteolytic cascades involved in tumor invasion and metastasis, these peptides might be useful lead molecules for the development of drugs for diseases associated with increased trypsin activity.

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Biological Chemistry keeps you up-to-date with all new developments in the molecular life sciences. In addition to original research reports, authoritative reviews written by leading researchers in the field keep you informed about the latest advances in the molecular life sciences. Rapid, yet rigorous reviewing ensures fast access to recent research results of exceptional significance in the biological sciences.

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general biochemistry
pathobiochemistry
structural biology
molecular and cellular biology
genetics and epigenetics
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cancer research
virology
immunology
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novel experimental methodologies

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