The Cytochrome P450 Engineering Database: integration of biochemical properties

<p>Abstract</p> <p>Background</p> <p>Cytochrome P450 monooxygenases (CYPs) form a vast and diverse enzyme class of particular interest in drug development and a high biotechnological potential. Although very diverse in sequence, they share a common structural fold. For the comprehensive and systematic comparison of protein sequences and structures the Cytochrome P450 Engineering Database (CYPED) was established. It was built up based on an extensible data model that enables its functions readily enhanced.</p> <p>Description</p> <p>The new version of the CYPED contains information on sequences and structures of 8613 and 47 proteins, respectively, which strictly follow Nelson's classification rules for homologous families and superfamilies. To gain biochemical information on substrates and inhibitors, the CYPED was linked to the Cytochrome P450 Knowledgebase (CPK). To overcome differences in the data model and inconsistencies in the content of CYPED and CPK, a metric was established based on sequence similarity to link protein sequences as primary keys. In addition, the annotation of structurally and functionally relevant residues was extended by a reliable prediction of conserved secondary structure elements and by information on the effect of single nucleotide polymorphisms.</p> <p>Conclusion</p> <p>The online accessible version of the CYPED at <url>http://www.cyped.uni-stuttgart.de</url> provides a valuable tool for the analysis of sequences, structures and their relationships to biochemical properties.</p

Funktionelle Charakterisierung der Signaltransduktionskaskade des LFA-1-Integrins

Die Aktivierung von T-Lymphozyten ist ein essentieller Prozeß für die Regulation der adaptiven Immunantwort. Hierbei werden in Folge einer Antigen-Exposition über verschiedene Oberflächenrezeptoren intrazelluläre Signaltransduktionsprozesse initiiert, welche in einer klonalen Expansion von T-Lymphozyten sowie deren Differenzierung zu Effektor- oder Gedächtniszellen resultieren. Die Spezifität dieser Prozesse wird durch die Wechselwirkung zwischen dem jeweiligen T-Zell-Antigenrezeptor (TCR) und einem Antigen-beladenen MHC-Molekül vermittelt, einer Interaktion, die allerdings nicht hinreichend für eine vollständige und dauerhafte Aktivierung der T-Zelle ist. Hierzu ist die Aktivierung sogenannter akzessorischer Oberflächenrezeptoren nötig, welche sowohl zur Verstärkung der Zell-Zell-Adhäsion als auch zur Induktion intrazellulärer Signalwege beitragen. Ein costimulatorisches Signal für naive T-Lymphozyten vermittelt zum Beispiel das CD28-Molekül, wodurch der Übergang dieser Zellen in einen anergischen Zustand verhindert und Zellproliferation ermöglicht wird. Zur Verstärkung der Zell-Zell-Interaktion tragen demgegenüber vor allem Adhäsionsmoleküle wie Selektine, Cadherine und Integrine bei. Der einzige Vertreter der β2-Integrinfamilie auf Lymphozyten, LFA-1, stand im Zentrum der im Folgenden beschriebenen Analysen. Es gab bereits Anhaltspunkte dafür, daß LFA-1 neben seiner Adhäsionsfunktion auch in Signaltransduktionsprozesse involviert ist. Allerdings sind die molekularen Mechanismen der LFA-1-vermittelten Signalwege bislang unvollständig charakterisiert. Dies liegt vor allem darin begründet, daß eine hochaffine Ligandenbindung erst nach einer Konformationsänderung des Integrins erfolgen kann. Eine solche Aktivierung des Integrins wird beispielsweise durch Stimulation der T-Lymphozyten über den T-Zell-Antigenrezeptor induziert, wodurch sich jedoch LFA-1-abhängige Signale mit denen des TCRs überlagern. Daher wurde im Verlauf der hier vorliegenden Arbeit ein auf Fusionsproteinen basierendes experimentelles System etabliert, welches eine aktivierungsunabhängige Untersuchung der LFA-1-vermittelten Signaltransduktion ermöglicht. Hierdurch wurde gezeigt, daß in humanen T-Lymphozyten die Aggregation der zytoplasmatischen Domäne der Integrin β2-Kette (CD18-Untereinheit) zur Erhöhung der intrazellulären Calciumkonzentration, zur IL-2-Promotoraktivierung sowie zum Anstiegs des Phosphotyrosingehalts zellulärer Proteine führte. Die Modulation dieser charakteristischen T-Zell- Aktivierungsparameter wird durch die zytoplasmatische Domäne der β2-Untereinheit von LFA-1 induziert, nicht aber durch die intrazellulären Anteile der Integrin αL- bzw. β1-Kette. Weiterhin konnte demonstriert werden, daß ein für die β2-Untereinheit spezifisches NPXFSequenzmotiv für deren Signalfunktion erforderlich ist. Dieselbe Region ist ebenso für die Signaltransduktion des nativen LFA-1-Gesamtmoleküls von elementarer Bedeutung. Überdies zeigten Untersuchungen in TCR-defizienten T-Zellen, daß die Oberflächenexpression des T-Zell-Rezeptors für den LFA-1-induzierten Signalweg essentiell ist. Demgegenüber erfolgte die intrazelluläre Calciummobilisierung durch das CD28-Molekül auch unabhängig von einer Expression des TCRs. Insgesamt konnte durch die vorliegenden Analysen die wesentliche Bedeutung des zytoplasmatischen Anteils der β2-Untereinheit des LFA-1-Integrins für den Prozeß der T-Zell-Aktivierung dokumentiert werden. Darüberhinaus wurde eine bisher unbekannte funktionelle Kooperativität zwischen LFA-1 und Komponenten des T-Zell-Antigenrezeptors aufgezeigt

Prediction and analysis of the modular structure of cytochrome P450 monooxygenases

<p>Abstract</p> <p>Background</p> <p>Cytochrome P450 monooxygenases (CYPs) form a vast and diverse family of highly variable sequences. They catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. Despite their differences in sequence and substrate specificity, the structures of CYPs are highly similar. Although being in research focus for years, factors mediating selectivity and activity remain vague.</p> <p>Description</p> <p>This systematic comparison of CYPs based on the Cytochrome P450 Engineering Database (<it>CYPED</it>) involved sequence and structure analysis of more than 8000 sequences. 31 structures have been applied to generate a reliable structure-based HMM profile in order to predict structurally conserved regions. Therefore, it was possible to automatically transfer these modules on CYP sequences without any secondary structure information, to analyze substrate interacting residues and to compare interaction sites with redox partners.</p> <p>Conclusions</p> <p>Functionally relevant structural sites of CYPs were predicted. Regions involved in substrate binding were analyzed in all sequences among the <it>CYPED</it>. For all CYPs that require a reductase, two reductase interaction sites were identified and classified according to their length. The newly gained insights promise an improvement of engineered enzyme properties for potential biotechnological application. The annotated sequences are accessible on the current version of the <it>CYPED</it>. The prediction tool can be applied to any CYP sequence via the web interface at <url>http://www.cyped.uni-stuttgart.de/cgi-bin/strpred/dosecpred.pl</url>.</p

The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases

Laccases and their homologues form the protein superfamily of multicopper oxidases (MCO). They catalyze the oxidation of many, particularly phenolic substances, and, besides playing an important role in many cellular activities, are of interest in biotechnological applications. The Laccase Engineering Database (LccED, http://www.lcced.uni-stuttgart.de) was designed to serve as a tool for a systematic sequence-based classification and analysis of the diverse multicopper oxidase protein family. More than 2200 proteins were classified into 11 superfamilies and 56 homologous families. For each family, the LccED provides multiple sequence alignments, phylogenetic trees and family-specific HMM profiles. The integration of structures for 14 different proteins allows a comprehensive comparison of sequences and structures to derive biochemical properties. Among the families, the distribution of the proteins regarding different kingdoms was investigated. The database was applied to perform a comprehensive analysis by MCO- and laccase-specific patterns

Investigation of Antimony in Natural Water and Leaching from Polyethylene Terephthalate (PET) Bottled Water

Abstract -Antimony (Sb) is one of the trace hazardous compounds in drinking water. Recent studies demonstrated that polyethylene terephthalate (PET) bottles can release antimony into water. It is also found on natural environment such as groundwater and crustal rocks. The natural content of Sb in northern Gyeonggi province in South Korea was very low range from 0.02~0.32 μg/L. The source water and tap water for 15 water supply plants from river or reservoir showed 0.13 μg/L on average. The groundwater concentration from 50 mineral springs indicated significantly low at 0.02 μg/L. The concentration of antimony was investigated in 47 bottled water brands on market. The average of Sb in bottled water brands was 0.57 μg/L. The detection rate was 100% in these products. Otherwise, raw water for bottled water contained 0.32 μg/L of antimony and detection rate was 90.7%. As a results of leaching experiment, antimony content in PET bottled water was increased from 1.04 to 9.84 μg/L under 60℃ after 12weeks. In case, the bottled water was stored in over 35℃, antimony leached into water. UV-ray irradiation to bottled water not induced increasing antimony release into water following 14days

The cytochrome P450 CYP6P4 is responsible for the high pyrethroid resistance in knockdown resistance-free Anopheles arabiensis.

Pyrethroid insecticides are the front line vector control tools used in bed nets to reduce malaria transmission and its burden. However, resistance in major vectors such as Anopheles arabiensis is posing a serious challenge to the success of malaria control. Herein, we elucidated the molecular and biochemical basis of pyrethroid resistance in a knockdown resistance-free Anopheles arabiensis population from Chad, Central Africa. Using heterologous expression of P450s in Escherichia coli coupled with metabolism assays we established that the over-expressed P450 CYP6P4, located in the major pyrethroid resistance (rp1) quantitative trait locus (QTL), is responsible for resistance to Type I and Type II pyrethroid insecticides, with the exception of deltamethrin, in correlation with field resistance profile. However, CYP6P4 exhibited no metabolic activity towards non-pyrethroid insecticides, including DDT, bendiocarb, propoxur and malathion. Combining fluorescent probes inhibition assays with molecular docking simulation, we established that CYP6P4 can bind deltamethrin but cannot metabolise it. This is possibly due to steric hindrance because of the large vdW radius of bromine atoms of the dihalovinyl group of deltamethrin which docks into the heme catalytic centre. The establishment of CYP6P4 as a partial pyrethroid resistance gene explained the observed field resistance to permethrin, and its inability to metabolise deltamethrin probably explained the high mortality from deltamethrin exposure in the field populations of this Sudano-Sahelian An. arabiensis. These findings describe the heterogeneity in resistance towards insecticides, even from the same class, highlighting the need to thoroughly understand the molecular basis of resistance before implementing resistance management/control tools

Bioinformatic Analysis Reveals High Diversity of Bacterial Genes for Laccase-Like Enzymes

Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three- domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)–0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter