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Regulation of G0 entry by the Pho80–Pho85 cyclin–CDK complex

Valeria Wanke, Ivo Pedruzzi, Elisabetta Cameroni, Frédérique Dubouloz, Claudio De Virgilio
2005 EMBO Journal  
et al, 2000 Pedruzzi et al, , 2003 Cameroni et al, 2004) .  ...  Consistent with our previous results, GFP-Rim15 C1176Y accumulates in the nuclei of glucose-limited and rapamycin-treated rim15D cells ( Figure 1A ; Pedruzzi et al, 2003) .  ... 
doi:10.1038/sj.emboj.7600889 pmid:16308562 pmcid:PMC1356330 fatcat:keqo5nsltjdubk6zmfklw3kjc4

Inactivation in vitro of theEscherichia coliouter membrane protein FhuA by a phage T5-encoded lipoprotein

Ivo Pedruzzi, Jurg P. Rosenbusch, Kaspar P. Locher
1998 FEMS Microbiology Letters  
Bacteriophage T5-encoded lipoprotein, synthesized by infected Escherichia coli cells, prevents superinfection of the host cell by this virus. The molecular basis of its ability to inactivate the receptor of phage T5, the FhuA protein, was investigated in vitro. Fully competent T5 lipoprotein, with a His tag attached to the C-terminus, was purified in detergent solution. Coreconstitution with homogeneous FhuA protein into liposomes revealed that the lipoprotein inhibited the irreversible
more » ... tion of phage T5 by FhuA protein. This phenomenon correlated with the inhibition of phage DNA ejection determined by fluorescence monitoring. Addition of detergent abolished the interaction between T5 lipoprotein and FhuA protein. When the signal sequence and N-terminal cysteinyl residue of the lipoprotein were removed by genetic truncation, the soluble polypeptide could be refolded and purified from inclusion bodies. The truncated lipoprotein interfered with infection of E. coli by phage T5, but only at very high concentrations. Circular dichroism spectra of both forms of T5 lipoprotein exhibited predominantly L-structure. T5 lipoprotein is sufficient for inactivation of the FhuA protein, presumably by inserting the Nterminal acyl chains into the membrane, thus increasing its local concentration. An in vitro stoichiometry of 10:1 has been calculated for the phage-encoded T5 lipoprotein to FhuA protein complex. z
doi:10.1111/j.1574-6968.1998.tb13264.x pmid:9812372 fatcat:4wdywztrefc3ha3gwfhgpwwaou

The Bud14p–Glc7p complex functions as a cortical regulator of dynein in budding yeast

Michèle Knaus, Elisabetta Cameroni, Ivo Pedruzzi, Kelly Tatchell, Claudio De Virgilio, Matthias Peter
2005 EMBO Journal  
doi:10.1038/sj.emboj.7600783 pmid:16107882 pmcid:PMC1201360 fatcat:sdr6jqulyfak3pwumipji2zs6q

HAMAP rules as SPARQL - A portable annotation pipeline for genomes and proteomes [article]

Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A Cuche, Andrea Auchincloss, Elisabeth COUDERT, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios (+2 others)
2019 bioRxiv   pre-print
., 2016] , and HAMAP [Pedruzzi et al., 2015] exploit information from experimentally characterized sequences to infer functions for uncharacterized homologs.  ... 
doi:10.1101/615294 fatcat:hivb7ymy3zeslmcgmrmnt4opti

Rim15 and the crossroads of nutrient signalling pathways in Saccharomyces cerevisiae

Erwin Swinnen, Valeria Wanke, Johnny Roosen, Bart Smets, Frédérique Dubouloz, Ivo Pedruzzi, Elisabetta Cameroni, Claudio De Virgilio, Joris Winderickx
2006 Cell Division  
In recent years, the general understanding of nutrient sensing and signalling, as well as the knowledge about responses triggered by altered nutrient availability have greatly advanced. While initial studies were directed to top-down elucidation of single nutrient-induced pathways, recent investigations place the individual signalling pathways into signalling networks and pursue the identification of converging effector branches that orchestrate the dynamical responses to nutritional cues. In
more » ... is review, we focus on Rim15, a protein kinase required in yeast for the proper entry into stationary phase (G0). Recent studies revealed that the activity of Rim15 is regulated by the interplay of at least four intercepting nutrient-responsive pathways.
doi:10.1186/1747-1028-1-3 pmid:16759348 pmcid:PMC1479807 fatcat:fhudmuyrsfbptm5rp5wpwbi4ve

TOR and PKA Signaling Pathways Converge on the Protein Kinase Rim15 to Control Entry into G0

Ivo Pedruzzi, Frédérique Dubouloz, Elisabetta Cameroni, Valeria Wanke, Johnny Roosen, Joris Winderickx, Claudio De Virgilio
2003 Molecular Cell  
., 1998; Pedruzzi et al., 2000; Garrett and of Rim15 appeared to occur even in the absence of Sch9 Broach, 1989).  ... 
doi:10.1016/s1097-2765(03)00485-4 pmid:14690612 fatcat:utmzuwokqjftzgt7eqr5hi5num

HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes

Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A Cuche, Andrea H Auchincloss, Elisabeth Coudert, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios (+2 others)
2020 GigaScience  
Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation. Here we demonstrate one approach to generate portable genome and proteome annotation pipelines
more » ... that users can run without recourse to custom software. This proof of concept uses our own rule-based annotation pipeline HAMAP, which provides functional annotation for protein sequences to the same depth and quality as UniProtKB/Swiss-Prot, and the World Wide Web Consortium (W3C) standards Resource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF Query Language). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to protein sequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation that is identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to any genome or proteome annotation pipeline. HAMAP SPARQL rules are freely available for download from the HAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available on GitHub at https://github.com/sib-swiss/HAMAP-SPARQL, and general documentation about HAMAP can be found on the HAMAP website at https://hamap.expasy.org.
doi:10.1093/gigascience/giaa003 pmid:32034905 pmcid:PMC7007698 fatcat:2wiy3bhoyndjrbosq6tsrrm5pq

HAMAP in 2015: updates to the protein family classification and annotation system

Ivo Pedruzzi, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Edouard de Castro, Delphine Baratin, Béatrice A. Cuche, Lydie Bougueleret, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios (+1 others)
2014 Nucleic Acids Research  
HAMAP (High-quality Automated and Manual Annotation of Proteins--available at http://hamap.expasy. org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the
more » ... pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm.
doi:10.1093/nar/gku1002 pmid:25348399 pmcid:PMC4383873 fatcat:ft6achqrt5cvdpgiwyrez7b3km

Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB

Marc Feuermann, Emmanuel Boutet, Anne Morgat, Kristian Axelsen, Parit Bansal, Jerven Bolleman, Edouard de Castro, Elisabeth Coudert, Elisabeth Gasteiger, Sébastien Géhant, Damien Lieberherr, Thierry Lombardot (+7 others)
2021 Metabolites  
The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers genomes and proteomes from tens of thousands of taxa, including a broad range of plants and microorganisms producing natural products of medical, nutritional, and agronomical interest. Here we describe work that enhances the utility of UniProtKB as a support for both the study of natural products and for their discovery. The foundation
more » ... this work is an improved representation of natural product metabolism in UniProtKB using Rhea, an expert-curated knowledgebase of biochemical reactions, that is built on the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Knowledge of natural products and precursors is captured in ChEBI, enzyme-catalyzed reactions in Rhea, and enzymes in UniProtKB/Swiss-Prot, thereby linking chemical structure data directly to protein knowledge. We provide a practical demonstration of how users can search UniProtKB for protein knowledge relevant to natural products through interactive or programmatic queries using metabolite names and synonyms, chemical identifiers, chemical classes, and chemical structures and show how to federate UniProtKB with other data and knowledge resources and tools using semantic web technologies such as RDF and SPARQL. All UniProtKB data are freely available for download in a broad range of formats for users to further mine or exploit as an annotation source, to enrich other natural product datasets and databases.
doi:10.3390/metabo11010048 pmid:33445429 pmcid:PMC7827101 fatcat:tatj2jy75refxbz3gqowk46nym

SwissBioPics—an interactive library of cell images for the visualization of subcellular location data

Philippe Le Mercier, Jerven Bolleman, Edouard de Castro, Elisabeth Gasteiger, Parit Bansal, Andrea H Auchincloss, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Anne Estreicher, Marc Feuermann, Damien Lieberherr (+4 others)
2022 Database: The Journal of Biological Databases and Curation  
SwissBioPics (www.swissbiopics.org) is a freely available resource of interactive, high-resolution cell images designed for the visualization of subcellular location data. SwissBioPics provides images describing cell types from all kingdoms of life—from the specialized muscle, neuronal and epithelial cells of animals, to the rods, cocci, clubs and spirals of prokaryotes. All cell images in SwissBioPics are drawn in Scalable Vector Graphics (SVG), with each subcellular location tagged with a
more » ... ue identifier from the controlled vocabulary of subcellular locations and organelles of UniProt (https://www.uniprot.org/locations/). Users can search and explore SwissBioPics cell images through our website, which provides a platform for users to learn more about how cells are organized. A web component allows developers to embed SwissBioPics images in their own websites, using the associated JavaScript and a styling template, and to highlight subcellular locations and organelles by simply providing the web component with the appropriate identifier(s) from the UniProt-controlled vocabulary or the 'Cellular Component' branch of the Gene Ontology (www.geneontology.org), as well as an organism identifier from the National Center for Biotechnology Information taxonomy (https://www.ncbi.nlm.nih.gov/taxonomy). The UniProt website now uses SwissBioPics to visualize the subcellular locations and organelles where proteins function. SwissBioPics is freely available for anyone to use under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. Database URL www.swissbiopics.org
doi:10.1093/database/baac026 pmid:35411389 pmcid:PMC9216577 fatcat:a4axqpsohnccfimw3gxvciws3i

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

Anke Burmester, Ekaterina Shelest, Gernot Glöckner, Christoph Heddergott, Susann Schindler, Peter Staib, Andrew Heidel, Marius Felder, Andreas Petzold, Karol Szafranski, Marc Feuermann, Ivo Pedruzzi (+16 others)
2011 Genome Biology  
Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.
more » ... ts: 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. Conclusions: Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.
doi:10.1186/gb-2011-12-1-r7 pmid:21247460 pmcid:PMC3091305 fatcat:cb3agm5g75alvdtbqbpmb2ygm4

Total thyroidectomy with ultrasonic scalpel: A multicenter, randomized controlled trial

Luiz P. Kowalski, Alvaro Sanabria, José Guilherme Vartanian, Roberto Araujo Lima, Ullianov Bezerra Toscano de Mendonca, Carlos Roberto dos Santos, Domingos Boldrini Júnior, Luis Eduardo Barbalho de Mello, Fernando Paiva Pinto, Carlos Neutzling Lehn, Luiz Artur Costa Correa, Rogério A. Dedivitis (+14 others)
2012 Head and Neck  
Background. The ultrasonic scalpel is a recently introduced device in head and neck surgery. Total thyroidectomy is the most common endocrine procedure performed by surgeons. Methods. This was an open, phase IV, multicenter, randomized controlled trial (RCT) that compared the use of an ultrasonic scalpel with a conventional technique in patients who underwent total thyroidectomy. The outcomes were surgical complication rate, operative time, drainage volume, postoperative pain, and costs.
more » ... . In all, 261 patients were included in 11 centers. There was a mean difference of 17% of operative time in favor of the ultrasonic scalpel group. There were no differences in postoperative complications. There was a difference in costs of 14% in favor of the ultrasonic scalpel group, but it was not statistically significant. Conclusions. The use of an ultrasonic scalpel was as safe as that of the conventional technique and had the advantage of a shorter operative time and lower postoperative drainage. Costs were not different between groups.
doi:10.1002/hed.21815 pmid:22302518 fatcat:6lxpbwhhlngypl6krgazkqeytu

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee (+122 others)
2020 Nucleic Acids Research  
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome
more » ... s and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
doi:10.1093/nar/gkaa1100 pmid:33237286 pmcid:PMC7778908 fatcat:6rwvp6l5uzb3li4lygf2gny6qq

A crowdsourcing open platform for literature curation in UniProt

Yuqi Wang, Qinghua Wang, Hongzhan Huang, Wei Huang, Yongxing Chen, Peter B. McGarvey, Cathy H. Wu, Cecilia N. Arighi, on behalf of the UniProt Consortium
2021 PLoS Biology  
Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, and Laure Verbregue  ...  Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo  ... 
doi:10.1371/journal.pbio.3001464 pmid:34871295 pmcid:PMC8675915 fatcat:6tsqu5evlre45ocilvfp4ad2ca

Bioinformatic Approach to Identify Penultimate Amino Acids Efficient for N-Terminal Methionine Excision

Sam Khalouei, Xiaoquan Yao, Jan Mennigen, Malisa Carullo, Pinchao Ma, Ziyu Song, Huiling Xiong, Xuhua Xia
2007 2007 1st International Conference on Bioinformatics and Biomedical Engineering  
Ivo Pedruzzi of Swiss-Prot helped us in identifying protein sequences with experimental evidence for NME. The first two authors contributed equally.  ... 
doi:10.1109/icbbe.2007.102 fatcat:stogg722bvfihofvp7kxjgnwi4
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