Solution Structure of a TBP–TAFII230 Complex Protein Mimicry of the Minor Groove Surface of the TATA Box Unwound by TBP

AbstractGeneral transcription factor TFIID consists of TATA box–binding protein (TBP) and TBP-associated factors (TAFIIs), which together play a central role in both positive and negative regulation of transcription. The N-terminal region of the 230 kDa Drosophila TAFII (dTAFII230) binds directly to TBP and inhibits TBP binding to the TATA box. We report here the solution structure of the complex formed by dTAFII230 N-terminal region (residues 11–77) and TBP. dTAFII23011–77 comprises three α helices and a β hairpin, forming a core that occupies the concave DNA-binding surface of TBP. The TBP-binding surface of dTAFII230 markedly resembles the minor groove surface of the partially unwound TATA box in the TBP–TATA complex. This protein mimicry of the TATA element surface provides the structural basis of the mechanism by which dTAFII230 negatively controls the TATA box–binding activity within the TFIID complex

Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain

ABSTRACT: Human TFIIB, an essential factor in transcription of protein-coding genes by RNA polymerase II, consists of an amino-terminal zinc binding domain (TFIIBn) connected by a linker of about 60 residues to a carboxy-terminal core domain (TFIIBc). The TFIIB core domain has two internally repeated motifs, each comprising five R-helices arranged as in the cyclin box. Compared to the crystal structure of TFIIBc in complex with TBP and a TATA-containing oligonucleotide, the NMR-derived solution structure of free TFIIBc is more compact, with a different repeat-repeat orientation and a significantly shorter first helix in the second repeat. Analysis of backbone 15 N relaxation parameters indicates the presence of relatively large amplitude, nanosecond time-scale motions in the TFIIBc interrepeat linker and structural fluctuations throughout the backbone. Interaction of TFIIBc with the acidic activation domain of VP16 or with TFIIBn induces 1 H-15 N chemical shift and line width changes concentrated in the first repeat, interrepeat linker and the first helix of the second repeat. These results suggest that TFIIB is somewhat pliable and that the conformation of the C-terminal core domain can be modulated by interaction with the N-terminal zinc binding domain. Furthermore, binding of the VP16 activation domain may promote TFIIBc conformations primed for binding to a TBP-DNA complex. TFIIB is an essential factor for initiation of transcription of protein-coding genes by RNA polymerase II (RNAPII), 1 one of the three eukaryotic nuclear RNA polymerases. Each of these polymerases requires a distinct set of auxiliary protein factors for specific initiation of RNA synthesis. In addition to TFIIB, the general initiation factors for RNAPII are TFIIA, TFIID [TATA binding protein (TBP) is a subunit of TFIID], TFIIE, TFIIF, and TFIIH (1-4). In the stepwise model for assembly of a transcription preinitiation complex (PIC) (1-3), TFIIB binds to the TBP (TFIID)-DNA complex and acts as a molecular bridge to RNAPII and the remaining initiation factors (5). TFIIB possesses sequencespecific DNA binding capacity for a DNA segment termed the IIB recognition element (BRE) immediately upstream of the TATA sequence of the adenovirus major late promoter Human TFIIB is a 316-residue polypeptid

Modeling and forecasting riverine dissolved inorganic nitrogen export using anthropogenic nitrogen inputs, hydroclimate, and land-use change

A quantitative understanding of riverine nitrogen (N) export in response to human activities and climate change is critical for developing effective watershed N pollution control measures. This study quantified net anthropogenic N inputs (NANI) and riverine dissolved inorganic N (DIN=NO3-N+NH4-N+NO2-N) export for the upper Jiaojiang River catchment in eastern China over the 1980-2010 time period and examined how NANI, hydroclimate, and land-use practices influenced riverine DIN export. Over the 31-yr study period, riverine DIN yield increased by 1.6-fold, which mainly results from a ~77% increase in NANI and increasing fractional delivery of NANI due to a ~55% increase in developed land area. An empirical model that utilizes an exponential function of NANI and a power function of combining annual water discharge and developed land area percentage could account for 89% of the variation in annual riverine DIN yields in 1980-2010. Applying this model, annual NANI, catchment storage, and natural background sources were estimated to contribute 57%, 22%, and 21%, respectively, of annual riverine DIN exports on average. Forecasting based on a likely future climate change scenario predicted a 19.6% increase in riverine DIN yield by 2030 due to a 4% increase in annual discharge with no changes in NANI and land-use compared to the 2000-2010 baseline condition. Anthropogenic activities have increased both the N inputs available for export and the fractional export of N inputs, while climate change can further enhance riverine N export. An integrated N management strategy that considers the influence of anthropogenic N inputs, land-use and climate change is required to effectively control N inputs to coastal areas

Reconstructing historical changes in phosphorus inputs to rivers from point and nonpoint sources in a rapidly developing watershed in eastern China, 1980–2010

Quantifying point (PS) and nonpoint source (NPS) phosphorus inputs to rivers is critical for developing effective watershed remediation strategies. This study reconstructed PS and NPS total phosphorus (TP) inputs to the Yongan River in eastern China in 1980-2010 using a load apportionment model (LAM) from paired riverine TP concentrations and river discharge records. Based on the fundamental hydrological differences between PS and NPS pollution, the LAM statistically quantified their individual inputs as a power-law function of river discharge. The LAM-estimated monthly/annual riverine TP loads were in good agreement with results derived from a regression model, Load Estimator (LOADEST). The annual TP load increased from 18.4 to 357.0 Mg yr(-1) between 1980 and 2010. The PS input contributed 7-45% of annual total TP load and increased 23-fold, consistent with a 20-fold increase in flow-adjusted average chloride concentration during the low flow regime (a proxy for wastewater inputs), as well as measured increases in population, poultry, and industrial production. Inferring from observed TP and chloride ratios, as well as total suspended solids (TSS) and river discharge dynamics, temporally retained P load within the river during the low flow regime was estimated to contribute 18-65% of the annual PS input load. NPS inputs consistently dominated the annual riverine TP load (55-93%) and increased 19-fold, consistent with the strong correlation between riverine TP and TSS concentrations, increasing developed land area, improved agricultural drainage systems, and phosphorus accumulation in agricultural soils. Based on our analysis, TP pollution control strategies should be preferentially directed at reductions in NPS loads, especially during summer high-flow periods when the greatest eutrophication risk occurs

Changes in river water temperature between 1980 and 2012 in Yongan watershed, eastern China: Magnitude, drivers and models

Climate warming is expected to have major impacts on river water quality, water column/hyporheic zone biogeochemistry and aquatic ecosystems. A quantitative understanding of spatio-temporal air (Ta) and water (Tw) temperature dynamics is required to guide river management and to facilitate adaptations to climate change. This study determined the magnitude, drivers and models for increasing Tw in three river segments of the Yongan watershed in eastern China. Over the 1980-2012 period, Tw in the watershed increased by 0.029-0.046°Cyr-1 due to a ~0.050°Cyr-1 increase of Ta and changes in local human activities (e.g., increasing developed land and population density and decreasing forest area). A standardized multiple regression model was developed for predicting annual Tw (R2=0.88-0.91) and identifying/partitioning the impact of the principal drivers on increasing Tw:Ta (76±1%), local human activities (14±2%), and water discharge (10±1%). After normalizing water discharge, climate warming and local human activities were estimated to contribute 81-95% and 5-19% of the observed rising Tw, respectively. Models forecast a 0.32-1.76°C increase in Tw by 2050 compared with the 2000-2012 baseline condition based on four future scenarios. Heterogeneity of warming rates existed across seasons and river segments, with the lower flow river and dry season demonstrating a more pronounced response to climate warming and human activities. Rising Tw due to changes in climate, local human activities and hydrology has a considerable potential to aggravate river water quality degradation and coastal water eutrophication in summer. Thus it should be carefully considered in developing watershed management strategies in response to climate change

Influence of Lag Effect, Soil Release, And Climate Change on Watershed Anthropogenic Nitrogen Inputs and Riverine Export Dynamics

This study demonstrates the importance of the nitrogen-leaching lag effect, soil nitrogen release, and climate change on anthropogenic N inputs (NANI) and riverine total nitrogen (TN) export dynamics using a 30-yr record for the Yongan River watershed in eastern China. Cross-correlation analysis indicated a 7-yr, 5-yr, and 4-yr lag time in riverine TN export in response to changes in NANI, temperature, and drained agricultural land area, respectively. Enhanced by warmer temperature and improved agricultural drainage, the upper 20 cm of agricultural soils released 270 kg N ha(-1) between 1980 and 2009. Climate change also increased the fractional export of NANI to river. An empirical model (R(2) = 0.96) for annual riverine TN flux incorporating these influencing factors estimated 35%, 41%, and 24% of riverine TN flux originated from the soil N pool, NANI, and background N sources, respectively. The model forecasted an increase of 45%, 25%, and 6% and a decrease of 13% in riverine TN flux from 2010 to 2030 under continued development, climate change, status-quo, and tackling scenarios, respectively. The lag effect, soil N release, and climate change delay riverine TN export reductions with respect to decreases in NANI and should be considered in developing and evaluating N management measures

Coupling stable isotopes and water chemistry to assess the role of hydrological and biogeochemical processes on riverine nitrogen sources.

Accurate source identification is critical for optimizing water pollution control strategies. Although the dual stable isotope (15N-NO3-/18O-NO3-) approach has been widely applied for differentiating riverine nitrogen (N) sources, the relatively short-term (<1 yr) 15N-NO3-/18O-NO3- records typically used in previous studies often hinders rigorous assessment due to high temporal variability associated with watershed N dynamics. Estimated contributions of legacy N sources in soils and groundwater to riverine N export by modeling approaches in many previous studies also lack validation from complementary information, such as multiple stable isotopes. This study integrated three years of multiple stable isotope (15N-NO3-/18O-NO3- and 2H-H2O/18O-H2O) and hydrochemistry measurements for river water, groundwater and rainfall to elucidate N dynamics and sources in the Yongan watershed (2474 km2) of eastern China. Nonpoint source N pollution dominated and displayed considerable seasonal and spatial variability in N forms and concentrations. Information from δ15N-NO3- and δ18O-NO3- indicated that riverine N dynamics were regulated by contributing sources, nitrification and denitrification, as well as hydrological processes. For the three examined catchments and entire watershed, slow subsurface and groundwater flows accounted for >75% of river discharge and were likely the major hydrological pathways for N delivery to the river. Riverine NO3- sources varied with dominant land use (p < 0.001), with the highest contributions of groundwater (60%), wastewater (35%), and soil (50%) occurring in agricultural, residential and forest catchments, respectively. For the entire watershed, groundwater (∼50%) and soil N (>30%) were the dominant riverine NO3- sources, implying considerable potential for N pollution legacy effects. Results were consistent with observed nitrous oxide dynamics and N sources identified in previous modeling studies. As the first attempt to apply multiple isotope tracers for exploring and quantifying N transformation and transport pathways, this study provides an integrated approach for verifying and understanding the N pollution legacy effects observed in many watersheds worldwide. This study highlights that river N pollution control in many watersheds requires particular attention to groundwater restoration and soil N management in addition to N input control strategies

Coupling stable isotopes and water chemistry to assess the role of hydrological and biogeochemical processes on riverine nitrogen sources.

Accurate source identification is critical for optimizing water pollution control strategies. Although the dual stable isotope (15N-NO3-/18O-NO3-) approach has been widely applied for differentiating riverine nitrogen (N) sources, the relatively short-term (<1 yr) 15N-NO3-/18O-NO3- records typically used in previous studies often hinders rigorous assessment due to high temporal variability associated with watershed N dynamics. Estimated contributions of legacy N sources in soils and groundwater to riverine N export by modeling approaches in many previous studies also lack validation from complementary information, such as multiple stable isotopes. This study integrated three years of multiple stable isotope (15N-NO3-/18O-NO3- and 2H-H2O/18O-H2O) and hydrochemistry measurements for river water, groundwater and rainfall to elucidate N dynamics and sources in the Yongan watershed (2474 km2) of eastern China. Nonpoint source N pollution dominated and displayed considerable seasonal and spatial variability in N forms and concentrations. Information from δ15N-NO3- and δ18O-NO3- indicated that riverine N dynamics were regulated by contributing sources, nitrification and denitrification, as well as hydrological processes. For the three examined catchments and entire watershed, slow subsurface and groundwater flows accounted for >75% of river discharge and were likely the major hydrological pathways for N delivery to the river. Riverine NO3- sources varied with dominant land use (p < 0.001), with the highest contributions of groundwater (60%), wastewater (35%), and soil (50%) occurring in agricultural, residential and forest catchments, respectively. For the entire watershed, groundwater (∼50%) and soil N (>30%) were the dominant riverine NO3- sources, implying considerable potential for N pollution legacy effects. Results were consistent with observed nitrous oxide dynamics and N sources identified in previous modeling studies. As the first attempt to apply multiple isotope tracers for exploring and quantifying N transformation and transport pathways, this study provides an integrated approach for verifying and understanding the N pollution legacy effects observed in many watersheds worldwide. This study highlights that river N pollution control in many watersheds requires particular attention to groundwater restoration and soil N management in addition to N input control strategies

Long-term (1980-2015) changes in net anthropogenic phosphorus inputs and riverine phosphorus export in the Yangtze River basin.

Quantitative information on long-term net anthropogenic phosphorus inputs (NAPI) and its relationship with riverine phosphorus (P) export are critical for developing sustainable and efficient watershed P management strategies. This is the first study to address long-term (1980-2015) NAPI and riverine P flux dynamics for the Yangtze River basin (YRB), the largest watershed in China. Over the 36-year study period, estimated NAPI to the YRB progressively increased by ∼1.4 times, with NAPIA (chemical fertilizer input + atmospheric deposition + seed input) and NAPIB (net food/feed imports + non-food input) contributing 65% and 35%, respectively. Higher population, livestock density and agricultural land area were the main drivers of increasing NAPI. Riverine total phosphorus (TP), particulate phosphorus (PP) and suspended sediment (SS) export at Datong hydrological station (downstream station) decreased by 52%, 75% and 75% during 1980-2015, respectively. In contrast, dissolved phosphorus (DP) showed an increase in both concentration (∼7-fold) and its contribution to TP flux (∼16-fold). Different trends in riverine P forms were mainly due to increasing dam/reservoir construction and changes in vegetation/land use and NAPI components. Multiple regression models incorporating NAPIA, NAPIB, dam/reservoir storage capacity and water discharge explained 84% and 92% of the temporal variability in riverine DP and PP fluxes, respectively. Riverine TP flux estimated as the sum of DP and PP fluxes showed high agreement with measured values (R2 = 0.87, NSE = 0.84), indicating strong efficacy for the developed models. The model forecasted an increase of 50% and 7% and a decrease of 15% and 22% in riverine DP flux from 2015 to 2045 under developing, dam building, NAPIA and NAPIB reduction scenarios, respectively. This study highlights the importance of including enhanced P transformation from particulate to bioavailable forms due to river regulation and changes in land-use, input sources and legacy P pools in development of P pollution control strategies