Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils

The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545–2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00792-016-0874-2) contains supplementary material, which is available to authorized users

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions