Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection

Cross-kingdom small RNA trafficking between hosts and microbes modulates gene expression in the interacting partners during infection. However, whether other RNAs are also transferred is unclear. Here, we discover that host plant Arabidopsis thaliana delivers mRNAs via extracellular vesicles (EVs) into the fungal pathogen Botrytis cinerea. A fluorescent RNA aptamer reporter Broccoli system reveals host mRNAs in EVs and recipient fungal cells. Using translating ribosome affinity purification profiling and polysome analysis, we observe that delivered host mRNAs are translated in fungal cells. Ectopic expression of two transferred host mRNAs in B. cinerea shows that their proteins are detrimental to infection. Arabidopsis knockout mutants of the genes corresponding to these transferred mRNAs are more susceptible. Thus, plants have a strategy to reduce infection by transporting mRNAs into fungal cells. mRNAs transferred from plants to pathogenic fungi are translated to compromise infection, providing knowledge that helps combat crop diseases.</p

Base de datos para factores de transcripción de Glycine max, Triticum aestivum y Zea maiz.

Los factores de transcripción (FTs) son proteínas que incrementan o disminuyen la tasa transcripcional de uno o varios genes. Los FTs desempeñan un papel fundamental en el control de casi todos los procesos biológicos: crecimiento, metabolismo, respuesta a factores ambientales, etc. En plantas cultivadas, son de particular importancia aquellos relacionados con la respuesta al estrés (sequía, salinidad, bajas temperaturas, plagas, enfermedades, etc.). La identificación de FTs, su posterior anotación y la construcción de bases de datos públicas constituye un importante recurso para el estudio de los procesos que controlan la expresión génica. Se construyó la base de datos FT-MTS que contiene información de 13,975 genes identificados como FTs en los genomas de Glycine max, Triticum aestivum y Zea maiz. Para ampliar la información sobre dichos FTs, se hizo una completa anotación que incluye: descripción de cada familia, alineamientos múltiples, dominios de unión, arquitectura de dominios, estructura 3D de proteínas homologas y grupos de ortólogos. Además, se incluyeron referencias a bases de datos externas que contienen descripción de dominios (Pfam), descripción de estructuras 3D (Protein Data Bank) y literatura relacionada (Pub-MED). Finalmente, se construyó una interfaz web (http://174.123.176.26:3000) que permite a los usuarios realizar búsquedas en la base de datos, descargar las secuencias de cada FT, descargar los alineamientos múltiples de cada dominio y comparar sus secuencias con las de los FTs vía BLAST o HMMER. _______________ TRANSCRIPTION FACTOR DATABASE OF GLYCINE MAX, TRITICUM AESTIVUM AND ZEA MAIZ. ABSTRACT: Transcription factors (TFs) are proteins that enhance or decrease the transcriptional rate of one of several genes. TFs play key roles regarding the control of almost all biologic processes: growth, metabolism, response to environmental facors, etc. In crop plants, TFs related to response to stress are particularly important (drought, salinity, low temperatures, plagues, plant diseases, etc.). Identification of TFs, their subsequent annotation and the construction of public databases constitute a valuable resource to study the processes that control genetic expression. A database named FT-MTS was built containing information about 13,975 genes identified as TFs in the Glycine max, Triticum aestivum y Zea maiz genomes. In order to broaden the information about those TFs, other data was recorded: description of every family, multiple sequence alignments, binding domains, domain architectures, 3D structure of homologous proteins and ortholog clusters. References to external databases containing domain descriptions (Pfam), 3D structure description (Protein Data Bank) and related literature (PubMED) were also included. A web interface p://174.123.176.26:3000) was built, so that users may search the data base, download the sequences for each TF and multiple sequence alignments of each domain, and compare their sequences with the TFs using BLAST or HMMER.Tesis (Maestría en Ciencias, especialista en Cómputo Aplicado).- Colegio de Postgraduados, 2012.Consejo Nacional de Ciencia y Tecnología (CONACYT)

Recuperación mejorada de hidrocarburos mediante desplazamiento miscible con CO2 en yacimientos naturalmente fracturados

Recuperación mejorada de hidrocarburos mediante desplazamiento miscible con CO2 en yacimientos naturalmente fracturado

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230 nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400 nt). Among subcellular compartments, membrane proteins are the largest (∼520 aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240 aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes

Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini)

Abstract Genetic diversity is the raw material of evolution, yet the reasons why it varies among species remain poorly understood. While studies at deeper phylogenetic scales point to the influence of life history traits on genetic diversity, it appears to be more affected by population size but less predictable at shallower scales. We used proxies for population size, mutation rate, direct selection, and linked selection to test factors affecting genetic diversity within a diverse assemblage of Neotropical salamanders, which vary widely for these traits. We estimated genetic diversity of noncoding loci using ddRADseq and coding loci using RNAseq for an assemblage of Neotropical salamanders distributed from northern Mexico to Costa Rica. Using ddRADseq loci, we found no significant association with genetic diversity, while for RNAseq data we found that environmental heterogeneity and proxies of population size predict a substantial portion of the variance in genetic diversity across species. Our results indicate that diversity of coding loci may be more predictable than that of noncoding loci, which appears to be mostly unpredictable at shallower phylogenetic scales. Our results suggest that coding loci may be more appropriate for genetic diversity estimates used in conservation planning because of the lack of any association between the variables we used and genetic diversity of noncoding loci