The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

Abstract Background Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC) plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN) is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.</p

Transcribing genes the hard way: in vitro reconstitution of nanoarchaeal RNA polymerase reveals unusual active site properties

Nanoarchaea represent a highly diverged archaeal phylum that displays many unusual biological features. The Nanoarchaeum equitans genome encodes a complete set of RNA polymerase (RNAP) subunits and basal factors. Several of the standard motifs in the active center contain radical substitutions that are normally expected to render the polymerase catalytically inactive. Here we show that, despite these unusual features, a RNAP reconstituted from recombinant Nanoarchaeum subunits is transcriptionally active. Using a sparse-matrix high-throughput screening method we identified an atypical stringent requirement for fluoride ions to maximize its activity under in vitro transcription conditions

From source to sink in the sediment cascade of the Hei-River Basin: Implications for late Quaternary landscape dynamics in the Gobi Desert, NW China

The Hei River Basin with a catchment size of ∼130,000 km2 is host to one of the largest continental alluvial fans in the world. The basin comprises: (1) its high-elevated river sources in the glacier and the permafrost zone of the Qilian Mountains, (2) the semi-arid foreland of the Hexi Corridor in the middle reaches and (3) the endorheic Ejina Basin (Gaxun Nur Basin) as its recent sink. The river basin is characterized by small subcatchments of hyper-arid mountain ranges of the Gobi-Tienshan and Beishan as well as of smooth and fuzzy water divides of the Hexi-Corridor and the Badain Jaran Sand Sea. Up to 300 m of Quaternary sediments establish the large Ejina Basin, with a size of 28,000 km2, as an excellent archive for environmental reconstructions located at the recent intersection of westerly and monsoonal air masses. Three sediment cores (up to 230 m long) provide evidence of sedimentation dynamics over the last 250,000 years, and cover at least two terminations since OIS 6. The sediments have to be regarded as a result of the interplay between tectonic activity and climate dynamics, accompanied by a related eolian and hydrological response of the catchment. Thus, it is crucial to understand and reconstruct the sedimentary processes along the huge sediment cascades, and to identify the most important sediment sources. Here we present a provenance analysis from mineralogical fingerprints of modern sediments that have been deposited along recent pathways from the sources to the Ejina Basin. The methodical approach combines the analysis of clay minerals, bulk mineralogy, and bulk geochemistry. Furthermore, we use heavy mineral data obtained from automated particle-analysis via a computer-controlled scanning electron microscope (CCSEM) and XRD measurements. We analyzed ∼200 surface samples from the whole catchment as reference material, aswell as the upper 19 m of cored sediments, to gain insight into temporal changes of depositional processes and provenance. Geostatistical analyses of the compositional data reveal a clear discrimination between sediments from the Qilian Shan in the south and from local basin sediments in the north. Moreover the mineralogical fingerprints allow the differentiation of sources from intrusive rocks that are dominant in the Bei Shan mountain sub-catchment, and from greenschist-bearing metamorphic rocks, that are widespread in the Qilian Mountain catchment. Finally, we draw conclusions about the main transport processes and pathways from assumed source regions to the sink (Ejina Basin). The provenance analysis of the sediment core reveals strong changes from local (Bei Shan) to long-distant (Qilian Shan) sources. The Late Pleistocene record reveals frequently changing sediment supply between periodic high mountain runoff and local episodic runoff. We assume that these variations are related to basin internal processes (e.g. fan dynamics, tectonics) and changing environmental conditions that are linked with variations in meltwater runoff and precipitation in the upper reaches of the southern catchment. These conclusions are supported by grain size characteristics that indicate phases of predominant alluvial activity and limnic deposition around the Late Glacial to Holocene transition and enhanced pre-Holocene eolian activity

Lake sediments documented late Quaternary humid pulses in the Gobi Desert of southern Mongolia: Vegetation, hydrologic and paleoglaciation inferences

Considerable efforts have been devoted to decipher the late Quaternary moisture and thermal history of the arid central Asia. However, an array of paramount aspects has inhibited our complete understanding of the broad pattern and underlying mechanisms: (i) Biased or even contradictory conclusions may be achieved due to the interpretations of different proxies. (ii) Most of the works poured attention into Holocene period, only few records can extend back to earlier marine isotope stages. (iii) Substantial spatial heterogeneity is noteworthy in the area. Exceeding amounts of studies were carried out in Lake Baikal catchments, northern and western Mongolia, while only two works were hitherto conducted in southern Mongolia. (iv) It remains elusive with respect to how and to what extent have East Asian Summer Monsoon and Westerlies affected the thermal and moisture signals in this spectacular arid region. To address this set of issues, two parallel cores (ONW I, 6.00 m; ONW II, 13.36 m) were retrieved from Orog Nuur, Gobi Desert of southern Mongolia. An array of multidisciplinary investigations involving geomorphologic mapping, radiocarbon dating, geochemical and biotic studies (i.e. palynological and ostracod valve analyses) provide a comprehensive data set for inferences of hydrological perturbations, vegetation development and phases of glacier expansions over the last ∼50 ka. Orog Nuur catchment depicted a broadly vulnerable ecosystem that was dominated by Artemisia steppe community in the late Pleistocene, and Chenopodiaceae desert steppe in the Holocene. In addition, the Termination I is ideally documented in a complete suite of geochemical, palynological, and ostracod signatures. In general, the thermal and moisture history in the Gobi Desert were as follows: (i) MIS3 had a relatively warm temperature and sufficient moisture supply in particular between ∼40 ka and ∼26 ka; (ii) The MIS2 was subject to cold temperature and moisture deficit, which was interrupted by two exceedingly cold and dry playa phases related to the LGM and YD; (iii) The Holocene exhibited a cool to milder temperature and considerable sufficient moisture supply in particular the early Holocene. In the eastern Khangai, the glacial expansion during MIS3 was slightly more notable than that during the LGM. The considerable humid pulse in the mid-to late-MIS3 may be the main driving mechanism for the MIS3 glacial advance. In central to southern Mongolia, rather than solely by the westerlies, the late Quaternary moisture and thermal history may be modulated, if not controlled, by coupled atmospheric components including both the westerlies and the penetration of the East Asian Summer Monsoon into the Asian interior. In addition, the two sand laminations (correspond to the LGM and YD event, respectively) recorded in the Orog Nuur may provide a potential opportunity to be regarded as chronological benchmarks for the lacustrine sequence in the Gobi Desert, albeit more investigations still need to be carried out to test its reliability in a larger spatial scale

Geomorphological Evidence of Active Faulting in Low Seismicity Regions - Examples From the Valley of Gobi Lakes, Southern Mongolia

Active intraplate deformation as a far-field effect of the India-Eurasia convergence has led to four Mw similar to 8 earthquakes in western and southern Mongolia in the past century. Palaeoseismological and morphotectonic studies have shown that these earthquakes are characteristic events along transpressive fault systems with cumulative offsets. The tectonically active Gobi Altai and Hangay mountains are separated by the seismically quiescent Valley of Gobi Lakes, which consists of major perennial rivers draining into endorheic lakes. Despite the scarcity of recorded earthquakes, Quaternary deposits in the Valley of Gobi Lakes are crosscut by multiple fault scarps with significant, landscape-altering displacements. To assess past earthquakes and the potential seismic hazard of this area, we apply remote sensing, tectono-morphometric techniques and cosmogenic nuclide dating to estimate the amount of deformation the faults in the Valley of Gobi Lakes are accommodating, and to determine the effect of these faults on local landscape evolution. The Tuyn Gol (gol = Mongolian for river) is crosscut by four E-W to NE-SW trending fault scarps that display variable fault kinematics due to scarp orientation differences relative to a stable NE-SW principle stress direction. Mapping of the >40-90 km long Valley of Gobi Lake faults shows that they can accommodate M similar to 7 earthquakes. Offset measurements of the Tuyn Gol deposits allow Middle Pleistocene to modern vertical slip rate estimates and M similar to 7 earthquake recurrence intervals of 0.012 +/- 0.007-0.13 +/- 0.07 mm/yr and 5.24 +/- 2.61-81.57 +/- 46.05 kyr, respectively. Cumulative vertical displacement amounts to 0.27 +/- 0.08 mm/yr, which is similar to that of major tectonic structures such as the Bogd fault in the Gobi Altai. This implies that the total active deformation accommodated by southern Mongolian faults may be larger than previously expected and distributed across more faults between the Hangay and the (Gobi) Altai mountain ranges. Geomorphological observations and surface exposure dating indicate that the Tuyn Gol drainage system developed over four to five 100 kyr climate cycles, during which active deformation played an important role in drainage reorganization. Our results demonstrate the dominant role of tectonics on local landscape dynamics, indicating the importance of studying regional geomorphology to adequately estimate the earthquake potential of faults that were considered inactive

Grain size and luminescence data from the Orog Nuur Basin (Mongolia)

The data comprise sample locations and results of grain size measurements and optically stimulated luminescence dating of sediments from the Orog Nuur Basin (southern Mongolia). Samples were taken in order to gain a comprehensive sedimentological and geochronological overview over late Quaternary sediment cascades and respective archives. Grain size measurements were conducted in Aachen using a Beckmann Coulter Laser Particle Sizer. OSL data were obtained in the Luminescence lab of Cologne University. Samples were classified into 7 sediment archives according to the field description and grain size analysis (fluvial, beach ridge, lacustrine, littoral sand, dune sand, basin silty sands, and mountain silt). The grain size statistics is presented in the .xlsx-table according to this classification. The combination of sedimentological, geomorphologic and geochronological observations led to a late Quaternary landscape reconstruction, including alluvial fan evolution, lake level history and aeolian dynamics in this arid region of the northern Gobi Desert