Mgm101: A double-duty Rad52-like protein

Mgm101 has well-characterized activity for the repair and replication of the mitochondrial genome. Recent work has demonstrated a further role for Mgm101 in nuclear DNA metabolism, contributing to an S-phase specific DNA interstrand cross-link repair pathway that acts redundantly with a pathway controlled by Pso2 exonuclease. Due to involvement of FANCM, FANCJ and FANCP homologues (Mph1, Chl1 and Slx4), this pathway has been described as a Fanconi anemia-like pathway. In this pathway, Mgm101 physically interacts with the DNA helicase Mph1 and the MutSα (Msh2/Msh6) heterodimer, but its precise role is yet to be elucidated. Data presented here suggests that Mgm101 functionally overlaps with Rad52, supporting previous suggestions that, based on protein structure and biochemical properties, Mgm101 and Rad52 belong to a family of proteins with similar function. In addition, our data shows that this overlap extends to the function of both proteins at telomeres, where Mgm101 is required for telomere elongation during chromosome replication in rad52 defective cells. We hypothesize that Mgm101 could, in Rad52-like manner, preferentially bind single-stranded DNAs (such as at stalled replication forks, broken chromosomes and natural chromosome ends), stabilize them and mediate single-strand annealing-like homologous recombination event to prevent them from converting into toxic structures.     

Niche analysis of orchids of serpentine and non-serpentine areas: Implications for conservation

Orchids are known for their species richness, intriguing ecology, rarity and the fact that they grow in almost all terrestrial ecosystems. Although numerous studies about their ecology have been carried out concerning calcareous areas, little is known about orchids that occur in serpentine habitats. The aim of this study was to investigate the ecological preferences of orchids in serpentine and non-serpentine areas on the model of the Valjevo Mountain Range (W Serbia). Niche analysis of orchids was performed using outlying mean index analysis. Data concerning geographical coordinates, altitude, habitat type, inclination, bedrock type, light regime, soil moisture, acidity, nitrogen and temperature were used as explanatory variables. Data of 33 orchid taxa from 407 localities were analysed. The most important gradients that govern orchid distribution were geological bedrock, light regime and temperature. The results have shown that only Anacamptis morio and Gymnadenia conopsea have statistically significantly larger populations on serpentine compared with non-serpentine bedrocks. This study highlights the importance of serpentine habitats as orchid habitats, bearing in mind the occurrence of rare species and species which were found exclusively in serpentine habitats.     

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

Abstract

Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in “V” shaped structures, recurrently observed in ribosomes and showing a high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their X-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behavior of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is its ability to investigate the region close to K-turn riboso- mal-like geometries. This part of the conformational space is not well characterized by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome.     

Activity of l,3-β-D-Glucanases in soil

Air-dried soil did not exhibit any measurable 1,3-β-D-glueanase activity. The enzyme activity was observed after a previous wetting of the soil or after supplementing it with glucose or caseine hydrolyzate. The addition of 1,3-β-D-glucan resulted in a significant increase of the enzyme activity in the variant with water and casein hydrolyzate but not in the variant treated with glucose.