EcoCyc: a comprehensive database resource for Escherichia coli

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions

The comprehensive updated regulatory network of Escherichia coli K-12

BACKGROUND: Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. coli transcription initiation and operons, providing in both the RegulonDB and EcoCyc databases the largest electronically encoded network available. A paper published recently by Ma et al. (2004) showed several differences in the versions of the network present in these two databases. Discrepancies have been corrected, annotations from this and other groups (Shen-Orr et al., 2002) have been added, making the RegulonDB and EcoCyc databases the largest comprehensive and constantly curated regulatory network of E. coli K-12. RESULTS: Several groups have been using these curated data as part of their bioinformatics and systems biology projects, in combination with external data obtained from other sources, thus enlarging the dataset initially obtained from either RegulonDB or EcoCyc of the E. coli K12 regulatory network. We kindly obtained from the groups of Uri Alon and Hong-Wu Ma the interactions they have added to enrich their public versions of the E. coli regulatory network. These were used to search for original references and curate them with the same standards we use regularly, adding in several cases the original references (instead of reviews or missing references), as well as adding the corresponding experimental evidence codes. We also corrected all discrepancies in the two databases available as explained below. CONCLUSION: One hundred and fifty new interactions have been added to our databases as a result of this specific curation effort, in addition to those added as a result of our continuous curation work. RegulonDB gene names are now based on those of EcoCyc to avoid confusion due to gene names and synonyms, and the public releases of RegulonDB and EcoCyc are henceforth synchronized to avoid confusion due to different versions. Public flat files are available providing direct access to the regulatory network interactions thus avoiding errors due to differences in database modelling and representation. The regulatory network available in RegulonDB and EcoCyc is the most comprehensive and regularly updated electronically-encoded regulatory network of E. coli K-12

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

RegulonDB is the internationally recognized reference database of Escherichia coli K-12 offering curated knowledge of the regulatory network and operon organization. It is currently the largest electronically-encoded database of the regulatory network of any free-living organism. We present here the recently launched RegulonDB version 5.0 radically different in content, interface design and capabilities. Continuous curation of original scientific literature provides the evidence behind every single object and feature. This knowledge is complemented with comprehensive computational predictions across the complete genome. Literature-based and predicted data are clearly distinguished in the database. Starting with this version, RegulonDB public releases are synchronized with those of EcoCyc since our curation supports both databases. The complex biology of regulation is simplified in a navigation scheme based on three major streams: genes, operons and regulons. Regulatory knowledge is directly available in every navigation step. Displays combine graphic and textual information and are organized allowing different levels of detail and biological context. This knowledge is the backbone of an integrated system for the graphic display of the network, graphic and tabular microarray comparisons with curated and predicted objects, as well as predictions across bacterial genomes, and predicted networks of functionally related gene products. Access RegulonDB at

Expression of the Azotobacter vinelandii Poly-β-Hydroxybutyrate Biosynthetic phbBAC Operon Is Driven by Two Overlapping Promoters and Is Dependent on the Transcriptional Activator PhbR

The Azotobacter vinelandii phbBAC genes encode the enzymes for poly-β-hydroxybutyrate (PHB) synthesis. The phbR gene, which is located upstream of and in the opposite direction of phbBAC, encodes PhbR, a transcriptional activator which is a member of the AraC family of activators. Here we report that a mutation in phbR reduced PHB accumulation and transcription of a phbB-lacZ fusion. We also report that phbB is transcribed from two overlapping promoters, p(B)1 and p(B)2. The region corresponding to the −35 region of p(B)1 overlaps the p(B)2 −10 region. In the phbR mutant, expression of phbB from the p(B)1 promoter is significantly reduced, whereas expression from the p(B)2 promoter is slightly increased. Two phbR promoters, p(R)1 and p(R)2, were also identified. Transcription from p(R)2 was shown to be dependent on σ(S). Six conserved 18-bp sites, designated R1 to R6, are present within the phbR-phbB intergenic region and are proposed to be putative binding targets for PhbR. R1 overlaps the −35 region of the p(B)1 promoter. A model for the regulation of phbB transcription by PhbR is proposed

Guía de evaluación a campo: Calidad estructural de suelos bajo siembra directa

La siembra directa (SD) es el principal sistema de manejo de suelos de la Argentina, y en particular de la Región Pampeana. Actualmente, el área cultivada bajo siembra directa representa aproximadamente el 90% del área total de cultivo nacional (31 millones de hectáreas). La SD es una herramienta clave en un esquema de agricultura conservacionista. Si bien esta práctica es fundamental para reducir la degradación del suelo, bajo determinados planteos puede conducir a incrementos en la resistencia mecánica, densificación y alteraciones en la estructura del horizonte superficial del suelo, como el desarrollo de estructuras laminares y masivas. En este contexto, la estructura del suelo es un componente clave de la fertilidad integral, por su influencia sobre el comportamiento físico, químico y biológico del suelo y por ello, sobre su capacidad de sustentar la productividad agrícola manteniendo la calidad ambiental. A pesar de que existen diferentes técnicas de laboratorio que permiten evaluar la estructura, las mismas son laboriosas y/o costosas. Por ello se ha avanzado en distintos métodos de evaluación de la estructura a campo, con diferentes variantes para su cuantificación. Sin embargo, las guías generadas hasta el momento han sido desarrolladas en ambientes edafo-climáticos diferentes a los de nuestras condiciones productivas. Asimismo, no están orientadas a suelos manejados bajo SD y suelen presentar un alto grado de subjetividad. Por lo tanto, estos métodos no necesariamente reflejan adecuadamente el estado de la estructura de nuestros suelos. Es por este motivo que surgió la necesidad de adaptar los métodos más utilizados de evaluación a campo de la estructura, a las particularidades de los suelos bajo SD de la región pampeana. Así surge la presente Guía, la cual permite evaluar cuantitativamente el estado de la estructura del suelo, ayudando a diagnosticar las posibles causas del deterioro físico y en base a esto, a desarrollar las estrategias adecuadas para el manejo de los suelos agrícolas de la región. La evaluación de la calidad estructural (ECE) a campo se realiza a través de metodologías sencillas, prácticas, de mínimo costo, y que demandan poco tiempo como el test de estallido y la evaluación de la presencia de estructuras laminares. Esta Guía ha sido desarrollada en suelos francos, franco arcillosos, franco arcillo-limosos y franco limosos de la región pampeana, bajo esquemas de agricultura extensiva en SD, por lo que su extrapolación a otros suelos, regiones o sistemas productivos exige tomar los recaudos, consideraciones y criterios agronómicos necesarios.Fil: Peralta, Guillermo Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bressan, Emiliano M. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; ArgentinaFil: Mortola, Natalia Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; ArgentinaFil: Romaniuk, Romina Ingrid. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; ArgentinaFil: Aciar, Leonardo Martín. Universidad Nacional de Salta; Facultad de Ciencias Naturales; ArgentinaFil: Agosti, Maria Belén. AAPRESID. GTD Chacra Pergamino; ArgentinaFil: Mousegne, Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Agencia de Extensión Rural San Antonio de Areco; ArgentinaFil: Gil, R.C. Instituto Nacional de tecnología Agropecuaria (INTA). Instituto de Suelos; Argentin

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their σ type, binding sites of specific transcriptional regulators (TRs), their organization into ‘regulatory phrases’, active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs. The current version has been expanded to include information beyond specific mechanisms aimed at gathering different growth conditions and the associated induced and/or repressed genes. RegulonDB is now linked with Swiss-Prot, with microarray databases, and with a suite of programs to analyze and visualize microarray experiments. We provide a summary of the biological knowledge contained in RegulonDB and describe the major changes in the design of the database. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/