Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

<p>Abstract</p> <p>Background</p> <p>In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the target. Key components of the RNAi systems are proteins of the Argonaute-PIWI family some of which function as slicers, the nucleases that cleave the target RNA that is base-paired to a guide RNA. Numerous prokaryotes possess the CRISPR-associated system (CASS) of defense against phages and plasmids that is, in part, mechanistically analogous but not homologous to eukaryotic RNAi systems. Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown.</p> <p>Results</p> <p>We present a detailed analysis of Argonaute-PIWI protein sequences and the genomic neighborhoods of the respective genes in prokaryotes. Whereas eukaryotic Ago/PIWI proteins always contain PAZ (oligonucleotide binding) and PIWI (active or inactivated nuclease) domains, the prokaryotic Argonaute homologs (pAgos) fall into two major groups in which the PAZ domain is either present or absent. The monophyly of each group is supported by a phylogenetic analysis of the conserved PIWI-domains. Almost all pAgos that lack a PAZ domain appear to be inactivated, and the respective genes are associated with a variety of predicted nucleases in putative operons. An additional, uncharacterized domain that is fused to various nucleases appears to be a unique signature of operons encoding the short (lacking PAZ) pAgo form. By contrast, almost all PAZ-domain containing pAgos are predicted to be active nucleases. Some proteins of this group (e.g., that from <it>Aquifex aeolicus</it>) have been experimentally shown to possess nuclease activity, and are not typically associated with genes for other (putative) nucleases. Given these observations, the apparent extensive horizontal transfer of pAgo genes, and their common, statistically significant over-representation in genomic neighborhoods enriched in genes encoding proteins involved in the defense against phages and/or plasmids, we hypothesize that pAgos are key components of a novel class of defense systems. The PAZ-domain containing pAgos are predicted to directly destroy virus or plasmid nucleic acids via their nuclease activity, whereas the apparently inactivated, PAZ-lacking pAgos could be structural subunits of protein complexes that contain, as active moieties, the putative nucleases that we predict to be co-expressed with these pAgos. All these nucleases are predicted to be DNA endonucleases, so it seems most probable that the putative novel phage/plasmid-defense system targets phage DNA rather than mRNAs. Given that in eukaryotic RNAi systems, the PAZ domain binds a guide RNA and positions it on the complementary region of the target, we further speculate that pAgos function on a similar principle (the guide being either DNA or RNA), and that the uncharacterized domain found in putative operons with the short forms of pAgos is a functional substitute for the PAZ domain.</p> <p>Conclusion</p> <p>The hypothesis that pAgos are key components of a novel prokaryotic immune system that employs guide RNA or DNA molecules to degrade nucleic acids of invading mobile elements implies a functional analogy with the prokaryotic CASS and a direct evolutionary connection with eukaryotic RNAi. The predictions of the hypothesis including both the activities of pAgos and those of the associated endonucleases are readily amenable to experimental tests.</p> <p>Reviewers</p> <p>This article was reviewed by Daniel Haft, Martijn Huynen, and Chris Ponting.</p

Study of the stochastic clustering on the refractory material surface under the effect of plasma load in the PLM device

Tungsten plates were tested in stationary helium discharges in the PLM device. The duration of discharges in the PLM reached 200 minutes. A distinctive feature of this device is the stationary plasma confinement, which is advantageous for testing fusion materials, including materials of the divertor and first wall of a fusion reactor. During plasma irradiation in the PLM, the thermal load on the surface of the tested plates was more than 1 MW/m(2). The temperature of the tested plates amounted to 1000 degrees C and more. Stochastic nanostructures with dimensions of the structural elements of less than 50 nm, including fuzz-type structures, were observed on the processed surfaces of the samples

Tillage erosion as an important driver of in‐field biomass patterns in an intensively used hummocky landscape

Tillage erosion causes substantial soil redistribution that can exceed water erosion especially in hummocky landscapes under highly mechanized large field agriculture. Consequently, truncated soil profiles can be found on hill shoulders and top slopes, whereas colluvial material is accumulated at footslopes, in depressions, and along downslope field borders. We tested the hypothesis that soil erosion substantially affects in-field patterns of the enhanced vegetation index (EVI) of different crop types on landscape scale. The interrelation between the EVI (RAPIDEYE satellite data; 5 m spatial resolution) as a proxy for crop biomass and modeled total soil erosion (tillage and water erosion modeled using SPEROS-C) was analyzed for the Quillow catchment (size: 196 km2) in Northeast Germany in a wet versus normal year for four crop types (winter wheat, maize, winter rapeseed, winter barley). Our findings clearly indicate that eroded areas had the lowest EVI values, while the highest EVI values were found in depositional areas. The differences in the EVI between erosional and depositional sites are more pronounced in the analyzed normal year. The net effect of total erosion on the EVI compared to areas without pronounced erosion or deposition ranged from −10.2% for maize in the normal year to +3.7% for winter barley in the wet year. Tillage erosion has been identified as an important driver of soil degradation affecting in-field crop biomass patterns in a hummocky ground moraine landscape. While soil erosion estimates are to be made, more attention should be given toward tillage erosion.ISSN:1085-3278ISSN:1099-145

Complex Risks from Old Urban Waste Landfills: Sustainability Perspective from Iasi, Romania

Landfills continue to represent the most frequent managerial practice for municipal solid wastes and an increasing and complex problem globally. In certain countries, a transition to an open society and free market is superimposed on the transition to sustainability, resulting in even higher complexity of management. This paper proposes an approach for problem-structuring of landfills in complex transitions: sustainability or unsustainability of a management approach is determined by a set of sustainability filters that are defined by sets of indicators and prioritized according the systemic concept of sustainability, which says that economy is embedded in society, which is embedded in nature. The writers exercise this approach with an old landfill in Iasi, Romania, and conclude for unsustainability, because the ecological sustainability filter is not successfully passed. Social and economic sustainability filters are also discussed in relation with the ecological sustainability indicators. The described approach allows a coherent, transdisciplinary synthesis of knowledge scattered across various disciplines, a pervasive problem in landfill management. The case study helps distinguish between generally true and context-dependent aspects.Peer reviewe

Development of Peptidomimetics Targeting IAPs

Inhibitor of apoptosis proteins (IAPs) such as XIAP subvert apoptosis by binding and inhibiting caspases. Because occupation of the XIAP BIR3 peptide binding pocket by Smac abolishes the XIAP–caspase 9 interaction, it is a proapoptotic event of great therapeutic interest. An assay for pocket binding was developed based on the displacement of Smac 7-mer from BIR3. Through the physical and biochemical analysis of a variety of peptides, we have determined the minimum sequence required for inhibition of the Smac–BIR3 interaction and detailed the dimensions and topology of the BIR3 peptide binding pocket. This work describes the structure–activity relationship (SAR) for peptide inhibitors of Smac-IAP binding