Inferring modules of functionally interacting proteins using the Bond Energy Algorithm

<p>Abstract</p> <p>Background</p> <p>Non-homology based methods such as phylogenetic profiles are effective for predicting functional relationships between proteins with no considerable sequence or structure similarity. Those methods rely heavily on traditional similarity metrics defined on pairs of phylogenetic patterns. Proteins do not exclusively interact in pairs as the final biological function of a protein in the cellular context is often hold by a group of proteins. In order to accurately infer modules of functionally interacting proteins, the consideration of not only direct but also indirect relationships is required.</p> <p>In this paper, we used the Bond Energy Algorithm (<it>BEA</it>) to predict functionally related groups of proteins. With <it>BEA </it>we create clusters of phylogenetic profiles based on the associations of the surrounding elements of the analyzed data using a metric that considers linked relationships among elements in the data set.</p> <p>Results</p> <p>Using phylogenetic profiles obtained from the Cluster of Orthologous Groups of Proteins (<it>COG</it>) database, we conducted a series of clustering experiments using <it>BEA </it>to predict (upper level) relationships between profiles. We evaluated our results by comparing with <it>COG's </it>functional categories, And even more, with the experimentally determined functional relationships between proteins provided by the <it>DIP </it>and <it>ECOCYC </it>databases. Our results demonstrate that <it>BEA </it>is capable of predicting meaningful modules of functionally related proteins. <it>BEA </it>outperforms traditionally used clustering methods, such as <it>k</it>-means and hierarchical clustering by predicting functional relationships between proteins with higher accuracy.</p> <p>Conclusion</p> <p>This study shows that the linked relationships of phylogenetic profiles obtained by <it>BEA </it>is useful for detecting functional associations between profiles and extending functional modules not found by traditional methods. <it>BEA </it>is capable of detecting relationship among phylogenetic patterns by linking them through a common element shared in a group. Additionally, we discuss how the proposed method may become more powerful if other criteria to classify different levels of protein functional interactions, as gene neighborhood or protein fusion information, is provided.</p

Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes

The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes

Transcription Analysis of Central Metabolism Genes in Escherichia coli. Possible Roles of σ38 in Their Expression, as a Response to Carbon Limitation

The phosphoenolpyruvate: carbohydrate transferase system (PTS) transports glucose in Escherichia coli. Previous work demonstrated that strains lacking PTS, such as PB11, grow slow on glucose. PB11 has a reduced expression of glycolytic, and upregulates poxB and acs genes as compared to the parental strain JM101, when growing on glucose. The products of the latter genes are involved in the production of AcetylCoA. Inactivation of rpoS that codes for the RNA polymerase σ38 subunit, reduces further (50%) growth of PB11, indicating that σ38 plays a central role in the expression of central metabolism genes in slowly growing cells. In fact, transcription levels of glycolytic genes is reduced in strain PB11rpoS− as compared to PB11. In this report we studied the role of σ70 and σ38 in the expression of the complete glycolytic pathway and poxB and acs genes in certain PTS− strains and their rpoS− derivatives. We determined the transcription start sites (TSSs) and the corresponding promoters, in strains JM101, PB11, its derivative PB12 that recovered its growth capacity, and in their rpoS− derivatives, by 5′RACE and pyrosequencing. In all these genes the presence of sequences resembling σ38 recognition sites allowed the proposition that they could be transcribed by both sigma factors, from overlapping putative promoters that initiate transcription at the same site. Fourteen new TSSs were identified in seventeen genes. Besides, more than 30 putative promoters were proposed and we confirmed ten previously reported. In vitro transcription experiments support the functionality of putative dual promoters. Alternatives that could also explain lower transcription levels of the rpoS− derivatives are discussed. We propose that the presence if real, of both σ70 and σ38 dependent promoters in all glycolytic genes and operons could allow a differential transcription of these central metabolism genes by both sigma subunits as an adaptation response to carbon limitation

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding of the regulatory circuits that control gene expression in this model organism. RegulonDB (http://regulondb.ccg.unam.mx/) is aimed at integrating the genetic regulatory network of E. coli K12 as an entirely bioinformatic project up till now. In this work, we extended its aims by generating experimental data at a genome scale on TSSs, promoters and regulatory regions. We implemented a modified 5′ RACE protocol and an unbiased High Throughput Pyrosequencing Strategy (HTPS) that allowed us to map more than 1700 TSSs with high precision. From this collection, about 230 corresponded to previously reported TSSs, which helped us to benchmark both our methodologies and the accuracy of the previous mapping experiments. The other ca 1500 TSSs mapped belong to about 1000 different genes, many of them with no assigned function. We identified promoter sequences and type of σ factors that control the expression of about 80% of these genes. As expected, the housekeeping σ70 was the most common type of promoter, followed by σ38. The majority of the putative TSSs were located between 20 to 40 nucleotides from the translational start site. Putative regulatory binding sites for transcription factors were detected upstream of many TSSs. For a few transcripts, riboswitches and small RNAs were found. Several genes also had additional TSSs within the coding region. Unexpectedly, the HTPS experiments revealed extensive antisense transcription, probably for regulatory functions. The new information in RegulonDB, now with more than 2400 experimentally determined TSSs, strengthens the accuracy of promoter prediction, operon structure, and regulatory networks and provides valuable new information that will facilitate the understanding from a global perspective the complex and intricate regulatory network that operates in E. coli

Ciencias Sociales: Economía y Humanidades

Este volumen I contiene 29 capítulos arbitrados que se ocupan de estos asuntos en Tópicos Selectos de Ciencias Sociales: Economía y Humanidades, elegidos de entre las contribuciones, reunimos algunos investigadores y estudiantes.Gómez, presenta un breve examen de la producción y comercialización de rosa en México; Arpi y Portillo realiza un estudio en México sobre el ingreso mínimo de las familias que identifica la línea de pobreza alimentaria en el área rural del sur de México, 2012; Bravo realiza un pequeño estudio donde hablará sobre el análisis comparado del Sector Gubernamental y la Economía Mexicana desde la perspectiva de los eslabonamientos productivos Hirshman-Rasmuss; Caamal, Pat, Jerónimo y Romero realizan un estudio sobre los canales de comercialización de limón persa en el municipio de Martínez de la Torre, Veracruz; Macías y Perales nos hablarán sobre una análisis del comercio estratégico en el TLCAN: El Estado en la política agrícola de biocombustibles; Figueroa, Pérez y Godínez se expresan acerca de la importancia de la comercialización del café en México; Sepúlveda, Sepúlveda y Pérez realizan un diagnóstico, retos del comercio electrónico en el Sector Agroindustrial Mexicano; Duana mediante su trabajo nos muestra y habla sobre la inversión extranjera directa y su impacto en crecimiento de México, un análisis en prospectiva: 1999-2010; Figueroa, Pérez y Ramírez hacen un estudio acerca sobre la importancia de la Banca en México; Pérez, Figueroa, Godínez y Pérez presenta un trabajo acerca de la competitividad de la producción agrícola en México, un análisis regional; Rodríguez, Espinosa y Márquez analizan todo acerca de el SIAL productor de quesos en Poxtla, competividad y territorio; Garza nos habla acerca de la intermediación financiera al servicio de la comunidad indígena: el fondo regional indígena Tarhiata Keri; Arroyo, Aguilar, Santoyo y Muñoz realizan un estudio acerca de la demanda de Importaciones de durazno (Prunus pérsica L. Batsch) en México procedentes de Estados Unidos de América (1982-2011); Loera y Sepúlveda analizan los parámetros de la productividad forestal en la producción de madera en rollo; Pérez, Morett y Tecpan realizan un análisis de factores sociales, ambientales y económicos del territorio rural cercano a la ciudad de México; Godínez, Figueroa y Pérez realizan un estudio acerca de la crisis económica mundial y su efecto sobre los flujos migratorios de América Latina; Magadán, Hernández y Escalona presentan la tipología de los sujetos sociales que intervienen en el mercado campesino de Ocotlán Oaxaca; Tavera y Cobos nos hablan de la normalización del proceso de compostaje: una opción para desarrollar el mercado de la composta; Piña y Pérez hablan acerca de la reestructuración del capitalismo y crisis política en México; Gonzáles, Rucoba y Ramírez realizan un estudio de la rentabilidad de la producción de miel en el municipio de León, Guanjuato; Ramírez, Gutiérrez y Figueroa realizan un estudio acerca de la economía del maíz en la región metropolitana, Chiapas, 2014; Bueno, Méndez y Cruz realizan un estudio y análisis de los centros de educación y cultura ambiental, necesidad de profesionalización Pedagógica de facilitadores ambientales; Pat, Caamal, Jerónimo y Mendoza presentan un estudio acerca de los Costos y competitividad de la producción del limón persa en el municipio de Martínez de la Torre, Veracruz. Vizuet presenta un trabajo de la construcción polisémica e histórica del concepto de la pobreza; Navarrete, Ríos y Arévalo presentan un estudio acerca de la producción ejidal de tomate rojo (Lycopersicum esculentum) en el DR-017, y su huella hídrica; Pérez y Piña hablan acerca de la productividad e inversión extranjera: La industria de Alimentos; Pérez, Figueroa, Godínez y Gómez presentan el trabajo sobre el sector primario en México; Pérez, Figueroa, Godínez y Gómez presentan acerca de los subsidios al campo como instrumento de política económica en México; Venegas, Perales y Del Valle realizan un estudio de rentabilidad de biodigestores y motogeneradores para diferentes tamaños de granjas porcinas en Michoacán

Ciencias Sociales: Economía y Humanidades HANDBOOK T-I

Se presenta un breve examen de la producción y comercialización de rosa en México; un estudio en México sobre el ingreso mínimo de las familias que identifica la línea de pobreza alimentaria en el área rural del sur de México, 2012; un pequeño estudio donde hablará sobre el análisis comparado del Sector Gubernamental y la Economía Mexicana desde la perspectiva de los eslabonamientos productivos Hirshman-Rasmuss; un estudio sobre los canales de comercialización de limón persa en el municipio de Martínez de la Torre, Veracruz; una análisis del comercio estratégico en el TLCAN: El Estado en la política agrícola de biocombustibles; también se expresan acerca de la importancia de la comercialización del café en México; un diagnóstico, retos del comercio electrónico en el Sector Agroindustrial Mexicano; trabajo nos muestra y habla sobre la inversión extranjera directa y su impacto en crecimiento de México, un análisis en prospectiva: 1999-2010; un estudio acerca sobre la importancia de la Banca en México; un trabajo acerca de la competitividad de la producción agrícola en México, un análisis regional; se analizan todo acerca de el SIAL productor de quesos en Poxtla, competividad y territorio; se habla acerca de la intermediación financiera al servicio de la comunidad indígena: el fondo regional indígena Tarhiata Keri; ademas un estudio acerca de la demanda de Importaciones de durazno (Prunus pérsica L. Batsch) en México procedentes de Estados Unidos de América (1982-2011); Loera y Sepúlveda analizan los parámetros de la productividad forestal en la producción de madera en rollo; un análisis de factores sociales, ambientales y económicos del territorio rural cercano a la ciudad de México; un estudio acerca de la crisis económica mundial y su efecto sobre los flujos migratorios de América Latina; Magadán, Hernández y Escalona presentan la tipología de los sujetos sociales que intervienen en el mercado campesino de Ocotlán Oaxaca; la normalización del proceso de compostaje: una opción para desarrollar el mercado de la composta; acerca de la reestructuración del capitalismo y crisis política en México; la rentabilidad de la producción de miel en el municipio de León, Guanjuato; la economía del maíz en la región metropolitana, Chiapas, 2014; análisis de los centros de educación y cultura ambiental, necesidad de profesionalización Pedagógica de facilitadores ambientales; los Costos y competitividad de la producción del limón persa en el municipio de Martínez de la Torre, Veracruz

Insights on the evolution of trehalose biosynthesis

Abstract Background The compatible solute trehalose is a non-reducing disaccharide, which accumulates upon heat, cold or osmotic stress. It was commonly accepted that trehalose is only present in extremophiles or cryptobiotic organisms. However, in recent years it has been shown that although higher plants do not accumulate trehalose at significant levels they have actively transcribed genes encoding the corresponding biosynthetic enzymes. Results In this study we show that trehalose biosynthesis ability is present in eubacteria, archaea, plants, fungi and animals. In bacteria there are five different biosynthetic routes, whereas in fungi, plants and animals there is only one. We present phylogenetic analyses of the trehalose-6-phosphate synthase (TPS) and trehalose-phosphatase (TPP) domains and show that there is a close evolutionary relationship between these domains in proteins from diverse organisms. In bacteria TPS and TPP genes are clustered, whereas in eukaryotes these domains are fused in a single protein. Conclusion We have demonstrated that trehalose biosynthesis pathways are widely distributed in nature. Interestingly, several eubacterial species have multiple pathways, while eukaryotes have only the TPS/TPP pathway. Vertebrates lack trehalose biosynthetic capacity but can catabolise it. TPS and TPP domains have evolved mainly in parallel and it is likely that they have experienced several instances of gene duplication and lateral gene transfer.</p