Impact of template backbone heterogeneity on RNA polymerase II transcription.

Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3'-5' or 2'-5' orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary 'imperfect' DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation

A century-scale, human-induced ecohydrological evolution of wetlands of two large river basins in Australia (Murray) and China (Yangtze)

Recently, the provision of food and water resources of two of the world's largest river basins, the Murray and the Yangtze, has been significantly altered through widespread landscape modification. Long-term sedimentary archives, dating back for some centuries from wetlands of these river basins, reveal that rapid, basin-wide development has reduced the resilience of biological communities, resulting in considerable decline in ecosystem services, including water quality. Large-scale human disturbance to river systems, due to river regulation during the mid-20th century, has transformed the hydrology of rivers and wetlands, causing widespread modification of aquatic biological communities. Changes to cladoceran zooplankton (water fleas) were used to assess the historical hydrology and ecology of three Murray and Yangtze river wetlands over the past century. Subfossil assemblages of cladocerans retrieved from sediment cores (94, 45, and 65 cm) of three wetlands: Kings Billabong (Murray), Zhangdu, and Liangzi lakes (Yangtze), showed strong responses to hydrological changes in the river after the mid-20th century. In particular, river regulation caused by construction of dams and weirs together with river channel modifications, has led to significant hydrological alterations. These hydrological disturbances were either (1) a prolonged inundation of wetlands or (2) reduced river flow, both of which caused variability in wetland depth. Inevitably, these phenomena have subsequently transformed the natural wetland habitats, leading to a switch in cladoceran assemblages to species preferring poor water quality, and in some cases to eutrophication. The quantitative and qualitative decline of wetland water conditions is indicative of reduced ecosystem services, and requires effective restoration measures for both river basins which have been impacted by recent socioeconomic development and climate change. © 2016 Author(s)

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation

Identifying sediment discontinuities and solving dating puzzles using monitoring and palaeolimnological records

Palaeolimnological studies should ideally be based upon continuous, undisturbed sediment sequences with reliable chronologies. However for some lake cores, these conditions are not met and palaeolimnologists are often faced with dating puzzles caused by sediment disturbances in the past. This study chooses Esthwaite Water from England to illustrate how to identify sedimentation discontinuities in lake cores and how chronologies can be established for imperfect cores by correlation of key sediment signatures in parallel core records and with long-term monitoring data (1945‒2003). Replicated short cores (ESTH1, ESTH7, and ESTH8) were collected and subjected to loss-on-ignition, radiometric dating (210Pb, 137Cs, and 14C), particle size, trace metal, and fossil diatom analysis. Both a slumping and a hiatus event were detected in ESTH7 based on comparisons made between the cores and the long-term diatom data. Ordination analysis suggested that the slumped material in ESTH7 originated from sediment deposited around 1805‒1880 AD. Further, it was inferred that the hiatus resulted in a loss of sediment deposited from 1870 to 1970 AD. Given the existence of three superior 14C dates in ESTH7, ESTH1 and ESTH7 were temporally correlated by multiple palaeolimnological proxies for age-depth model development. High variability in sedimentation rates was evident, but good agreement across the various palaeolimnological proxies indicated coherence in sediment processes within the coring area. Differences in sedimentation rates most likely resulted from the natural morphology of the lake basin. Our study suggests that caution is required in selecting suitable coring sites for palaeolimnological studies of small, relatively deep lakes and that proximity to steep slopes should be avoided wherever possible. Nevertheless, in some cases, comparisons between a range of contemporary and palaeolimnological records can be employed to diagnose sediment disturbances and establish a chronology

Early warning of critical transitions in biodiversity from compositional disorder

Global environmental change presents a clear need for improved leading indicators of critical transitions, especially those that can be generated from compositional data and that work in empirical cases. Ecological theory of community dynamics under environmental forcing predicts an early replacement of slowly replicating and weakly competitive “canary” species by slowly replicating but strongly competitive “keystone” species. Further forcing leads to the eventual collapse of the keystone species as they are replaced by weakly competitive but fast‐replicating “weedy” species in a critical transition to a significantly different state. We identify a diagnostic signal of these changes in the coefficients of a correlation between compositional disorder and biodiversity. Compositional disorder measures unpredictability in the composition of a community, while biodiversity measures the amount of species in the community. In a stochastic simulation, sequential correlations over time switch from positive to negative as keystones prevail over canaries, and back to positive with domination of weedy species. The model finds support in empirical tests on multi‐decadal time series of fossil diatom and chironomid communities from lakes in China. The characteristic switch from positive to negative correlation coefficients occurs for both communities up to three decades preceding a critical transition to a sustained alternate state. This signal is robust to unequal time increments that beset the identification of early‐warning signals from other metrics

Deciphering long-term records of natural variability and human impact as recorded in lake sediments: a palaeolimnological puzzle

Global aquatic ecosystems are under increasing threat from anthropogenic activity, as well as being exposed to past (and projected) climate change, however, the nature of how climate and human impacts are recorded in lake sediments is often ambiguous. Natural and anthropogenic drivers can force a similar response in lake systems, yet the ability to attribute what change recorded in lake sediments is natural, from that which is anthropogenic, is increasingly important for understanding how lake systems have, and will continue to function when subjected to multiple stressors; an issue that is particularly acute when considering management options for aquatic ecosystems. The duration and timing of human impacts on lake systems varies geographically, with some regions of the world (such as Africa and South America) having a longer legacy of human impact than others (e.g., New Zealand). A wide array of techniques (biological, chemical, physical and statistical) is available to palaeolimnologists to allow the deciphering of complex sedimentary records. Lake sediments are an important archive of how drivers have changed through time, and how these impacts manifest in lake systems. With a paucity of ‘real-time’ data pre-dating human impact, palaeolimnological archives offer the only insight into both natural variability (i.e., that driven by climate and intrinsic lake processes) and the impact of people. While there is a need to acknowledge complexity, and temporal and spatial variability when deciphering change from sediment archives, a palaeolimnological approach is a powerful tool for better understanding and managing global aquatic resources