ATP-dependent G-quadruplex unfolding by Bloom helicase exhibits low processivity

Various helicases and single stranded DNA (ssDNA) binding proteins unfold G-quadruplex (GQ) structures. However, the underlying mechanisms of this activity have only recently come to focus. We report kinetic studies on Bloom (BLM) helicase and human telomeric GQ interactions using single-molecule Förster resonance energy transfer (smFRET). Using partial duplex DNA (pdDNA) constructs with different 5′ ssDNA overhangs, we show that BLM localizes in the vicinity of ssDNA/double-stranded DNA (dsDNA) junction and reels in the ssDNA overhang in an ATP-dependent manner. A comparison of DNA constructs with or without GQ in the overhang shows that GQ unfolding is achieved in 50–70% of reeling attempts under physiological salt and pH conditions. The unsuccessful attempts often result in dissociation of BLM from DNA which slows down the overall BLM activity. BLM-mediated GQ unfolding is typically followed by refolding of the GQ, a pattern that is repeated several times before BLM dissociates from DNA. BLM is significantly less processive compared to the highly efficient GQ destabilizer Pif1 that can repeat GQ unfolding activity hundreds of times before dissociating from DNA. Despite the variations in processivity, our studies point to possible common patterns used by different helicases in minimizing the duration of stable GQ formation.     

Response of wheat genotypes to sowing date and boron fertilization aimed at controlling sterility in a rice-wheat rotation in Nepal

Spikelet sterility in wheat (Triticum aestivum L.) is emerging as a production threat in different parts of Nepal. This study was aimed at determining the effects of sowing date and boron application in controlling spikelet sterility in four different genotypes of spring wheat in a rice-wheat system in the western hills of Nepal. Four genotypes of known different responses to boron were planted on 21 November, 6 December and 21 December, 1994 with or without boron application at 1 kg B ha-1 (i.e. 9 kg borax ha-1) on a soil that was known to be deficient in boron.The effect of sowing date was significant for the phenology, yield components, percentage sterility and grain yield. Sterility was significantly increased in the crop planted on 21 December, which had also the lowest 1000 seed weight and grain yield; there was an almost 50% grain yield reduction compared to the crop planted on 21 November. Terminal moisture stress (i.e. lack of moisture during the later part of the development) was observed in the late sown crop which also amplified the extent of sterility associated with boron deficiency. Genotypes differed in response to sowing dates and boron treatment for all of the phenological events measured, yield components, grain yield and percentage sterility. SW-41 and BL-1022 had significantly higher sterility at all sowing dates. BL-1249 showed a consistently lower% sterility over all sowing dates and boron treatments. The addition of boron significantly increased the number of grains set per spike thereby decreasing the total sterility in boron responsive genotypes SW-41 and BL-1022 while those not susceptible did not respond. The boron concentration in the flag leaf at anthesis was increased in treatments with added B in the soil but genotypes did not differ in boron concentration for any soil treatment.     

RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP

Various helicases and single-stranded DNA (ssDNA) binding proteins are known to destabilize G-quadruplex (GQ) structures, which otherwise result in genomic instability. Bulk biochemical studies have shown that Bloom helicase (BLM) unfolds both intermolecular and intramolecular GQ in the presence of ATP. Using single molecule FRET, we show that binding of RecQ-core of BLM (will be referred to as BLM) to ssDNA in the vicinity of an intramolecular GQ leads to destabilization and unfolding of the GQ in the absence of ATP. We show that the efficiency of BLM-mediated GQ unfolding correlates with the binding stability of BLM to ssDNA overhang, as modulated by the nucleotide state, ionic conditions, overhang length and overhang directionality. In particular, we observed enhanced GQ unfolding by BLM in the presence of non-hydrolysable ATP analogs, which has implications for the underlying mechanism. We also show that increasing GQ stability, via shorter loops or higher ionic strength, reduces BLM-mediated GQ unfolding. Finally, we show that while WRN has similar activity as BLM, RecQ and RECQ5 helicases do not unfold GQ in the absence of ATP at physiological ionic strength. In summary, our study points to a novel and potentially very common mechanism of GQ destabilization mediated by proteins binding to the vicinity of these structures.     

Geographic selection bias of occurrence data influences transferability of invasive Hydrilla verticillata distribution models

Due to socioeconomic differences, the accuracy and extent of reporting on the occurrence of native species differs among countries, which can impact the performance of species distribution models. We assessed the importance of geographical biases in occurrence data on model performance using Hydrilla verticillata as a case study. We used Maxent to predict potential North American distribution of the aquatic invasive macrophyte based upon training data from its native range. We produced a model using all available native range occurrence data, then explored the change in model performance produced by omitting subsets of training data based on political boundaries. We also compared those results with models trained on data from which a random sample of occurrence data was omitted from across the native range. Although most models accurately predicted the occurrence of H. verticillata in North America (AUC > 0.7600), data omissions influenced model predictions. Omitting data based on political boundaries resulted in larger shifts in model accuracy than omitting randomly selected occurrence data. For well‐documented species like H. verticillata, missing records from single countries or ecoregions may minimally influence model predictions, but for species with fewer documented occurrences or poorly understood ranges, geographic biases could misguide predictions. Regardless of focal species, we recommend that future species distribution modeling efforts begin with a reflection on potential spatial biases of available occurrence data. Improved biodiversity surveillance and reporting will provide benefit not only in invaded ranges but also within under‐reported and unexplored native ranges.