Nucleosomes affect local transformation efficiency

Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency

Caracterización molecular y conservación de hongos del suelo asociados con la respuesta a estrés por nitrógeno

La fijación biológica del Nitrógeno es un proceso que aporta con un 65% de fijación anual de nitrógeno al ecosistema; ejecutada por microorganismos fúngicos capaces de reducir la forma atmosférica del N en una forma asimilable. Existen varias actividades antrópicas que han favorecido el aumento de la adicción de N, lo que ha generado la duplicación de la cantidad que es incorporada por año en los diferentes ciclos biológicos de la tierra. El presente estudio tiene como objetivo caracterizar molecularmente y criopreservar hongos asociados con la respuesta al estrés por N. Se seleccionaron suelos sometidos a un alto estrés por adicción sostenida de N junto a suelos control, de los cuales se aisló los hongos cultivables para ser caracterizados y clasificados morfológicamente a través de técnicas moleculares. Obteniendo como resultado 43 cepas caracterizadas por morfología básica (color, forma y tamaño). Por medio de la secuencia del gen ITS ARN ribosomal, la filogenia indicó la presencia del Phylum Ascomycota con dos clados: Eurotiales con los siguientes géneros (Penicillium, Citrinum, y Aspergillus). El clado Hypocreales presenta los géneros (Metarrhzium, Clonostachys y Tolypocladium) y el Phylum Zygomycota con el género Morlierella. El porcentaje de reactivación de las cepas criopreservadas fue de 98%

Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles

Escherichia coli K12 is a commensal bacteria and one of the best-studied model organisms. Salmonella enterica serovar Typhimurium, on the other hand, is a facultative intracellular pathogen. These two prokaryotic species can be considered related phylogenetically and they share a large amount of their genetic material, which is commonly termed the 'core genome'. Despite their shared core genome, both species display very different life styles and it is unclear to what extent the core genome, apart from the species-specific genes, plays a role in this lifestyle divergence. In this study, we focus on the differences in expression domains for the orthologous genes in E. coli and S. Typhimurium. The iterative comparison of coexpression methodology was used on large expression compendia of both species to uncover the conservation and divergence of gene expression. We found that gene expression conservation occurs mostly independent from amino acid similarity. According to our estimates, at least more than one quarter of the orthologous genes has a different expression domain in E. coli than in S. Typhimurium. Genes involved with key cellular processes are most likely to have conserved their expression domains whereas genes showing diverged expression are associated with metabolic processes that, although present in both species, are regulated differently. The expression domains of the shared 'core' genome of E. coli and S. Typhimurium, consisting of highly conserved orthologs, have been tuned to help accommodate the differences in lifestyle and the pathogenic potential of Salmonella.status: publishe

Proximity-based cis-regulatory module detection using constraint programming for itemset mining

cis-regulatory modules (CRMs) are combinations of Transcription Factor Binding Sites involved in the regulation of genes. The detection of CRMs is key in developing a better understanding of gene regulation. Identifying significant combinations of binding sites is a difficult computational problem. Existing techniques use heuristic methods or strong restrictions to make the problem tractable, and are not very extendible. We present an extendible technique for enumerating all potential CRMs using only a biologically well-motivated restriction on the proximity of the binding sites involved. Our method consists of 3 phases: First, the genomic sequences under investigation are screened using an existing library of motif models, namely, position weight matrices. This screening identifies Transcription Factor Binding Site (TFBS) hits. Secondly, we use constraint programming for itemset mining to efficiently enumerate all combinations of TFBS hits that co-occur within a pre-defined distance, while avoiding undesirable redundancies. This results in an exhaustive list of potential CRMs. Lastly, the CRMs are ranked using statistical methodsstatus: publishe

Genetic and functional characterization of cyclic lipopeptide white-line-inducing principle (WLIP) production by rice rhizosphere isolate Pseudomonas putida RW10S2

The secondary metabolite mediating the GacS-dependent growth-inhibitory effect exerted by the rice rhizosphere isolate Pseudomonas putida RW10S2 on phytopathogenic Xanthomonas species was identified as white-line-inducing principle (WLIP), a member of the viscosin group of cyclic lipononadepsipeptides. WLIP producers are commonly referred to by the taxonomically invalid name “Pseudomonas reactans,” based on their capacity to reveal the presence of a nearby colony of Pseudomonas tolaasii by inducing the formation of a visible precipitate (“white line”) in agar medium between both colonies. This phenomenon is attributed to the interaction of WLIP with a cyclic lipopeptide of a distinct structural group, the fungitoxic tolaasin, and has found application as a diagnostic tool to identify tolaasin-producing bacteria pathogenic to mushrooms. The genes encoding the WLIP nonribosomal peptide synthetases WlpA, WlpB, and WlpC were identified in two separate genomic clusters (wlpR-wlpA and wlpBC) with an operon organization similar to that of the viscosin, massetolide, and entolysin biosynthetic systems. Expression of wlpR is dependent on gacS, and the encoded regulator of the LuxR family (WlpR) activates transcription of the biosynthetic genes and the linked export genes, which is not controlled by the RW10S2 quorum-sensing system PmrR/PmrI. In addition to linking the known phenotypes of white line production and hemolytic activity of a WLIP producer with WLIP biosynthesis, additional properties of ecological relevance conferred by WLIP production were identified, namely, antagonism against Xanthomonas and involvement in swarming and biofilm formation

An Efficient Method for the Extraction of High-Quality Fungal Total RNA to Study the Mycosphaerella fijiensis-Musa spp. Interaction

Efficient RNA isolation is a prerequisite for gene expression studies and it has an increasingly important role in the study of plant-fungal pathogen interactions. However, RNA isolation is difficult in filamentous fungi. These organisms are notorious for their rigid cell walls and the presence of high levels of carbohydrates, excreted from the fungal cells during submerged growth, which interferes with the extraction procedures. Although many commercial kits are already available for RNA isolation, they do not provide, in most cases, enough amount of pure RNA to be used in upstream applications. In the present work, we propose an easy and efficient protocol for isolating total RNA from the filamentous fungus Mycosphaerella fijiensis, the most important foliar pathogen of Musa spp. varieties worldwide. In addition, we applied the proposed protocol to the isolation of total RNA from banana leaves infected with the pathogen. Our methodology was developed based on the SDS method with modifications including a carbohydrate precipitation step. The protocol resulted in high-quality total RNA, from fungal mycelium grown in PDB medium and infected banana leaves, suitable for further molecular studies. The proposed methodology is also applicable to the ascomycete fungus Passalora fulva (syn. Cladosporum fulvum).status: publishe

Genetic and functional characterization of cyclic lipopeptide white-line-inducing principle (WLIP) production by rice rhizosphere isolate pseudomonas putida RW10S2

The secondary metabolite mediating the GacS-dependent growth-inhibitory effect exerted by the rice rhizosphere isolate Pseudomonas putida RW10S2 on phytopathogenic Xanthomonas species was identified as white-line-inducing principle (WLIP), a member of the viscosin group of cyclic lipononadepsipeptides. WLIP producers are commonly referred to by the taxonomically invalid name "Pseudomonas reactans," based on their capacity to reveal the presence of a nearby colony of Pseudomonas tolaasii by inducing the formation of a visible precipitate ("white line") in agar medium between both colonies. This phenomenon is attributed to the interaction of WLIP with a cyclic lipopeptide of a distinct structural group, the fungitoxic tolaasin, and has found application as a diagnostic tool to identify tolaasin-producing bacteria pathogenic to mushrooms. The genes encoding the WLIP nonribosomal peptide synthetases WlpA, WlpB, and WlpC were identified in two separate genomic clusters (wlpR-wlpA and wlpBC) with an operon organization similar to that of the viscosin, massetolide, and entolysin biosynthetic systems. Expression of wlpR is dependent on gacS, and the encoded regulator of the LuxR family (WlpR) activates transcription of the biosynthetic genes and the linked export genes, which is not controlled by the RW10S2 quorum-sensing system PmrR/PmrI. In addition to linking the known phenotypes of white line production and hemolytic activity of a WLIP producer with WLIP biosynthesis, additional properties of ecological relevance conferred by WLIP production were identified, namely, antagonism against Xanthomonas and involvement in swarming and biofilm formation.status: publishe

Nucleosomes affect local transformation efficiency

Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.status: publishe

MAGIC: access portal to a cross-platform gene expression compendium for maize

To facilitate the exploration of publicly available Zea mays expression data, we constructed a maize expression compendium, making use of an integration methodology and a consistent probe to gene mapping based on the 5b.60 sequence release of Z. mays. The compendium is made available through a web portal MAGIC that hosts a variety of analysis tools to easily browse and analyze the data. Our compendium is different from previous initiatives in combining expression values across different experiments by providing a consistent gene annotation across different platforms

Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast

Bulk segregant analysis (BSA) coupled to high throughput sequencing is a powerful method to map genomic regions related with phenotypes of interest. It relies on crossing two parents, one inferior and one superior for a trait of interest. Segregants displaying the trait of the superior parent are pooled, the DNA extracted and sequenced. Genomic regions linked to the trait of interest are identified by searching the pool for overrepresented alleles that normally originate from the superior parent. BSA data analysis is non-trivial due to sequencing, alignment and screening errors.status: publishe