Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling

Previous work in yeast has suggested that modification of tRNAs, in particular uridine bases in the anticodon wobble position (U34), is linked to TOR (target of rapamycin) signaling. Hence, U34 modification mutants were found to be hypersensitive to TOR inhibition by rapamycin. To study whether this involves inappropriate TOR signaling, we examined interaction between mutations in TOR pathway genes (tip41Δ, sap190Δ, ppm1Δ, rrd1Δ) and U34 modification defects (elp3Δ, kti12Δ, urm1Δ, ncs2Δ) and found the rapamycin hypersensitivity in the latter is epistatic to drug resistance of the former. Epistasis, however, is abolished in tandem with a gln3Δ deletion, which inactivates transcription factor Gln3 required for TOR-sensitive activation of NCR (nitrogen catabolite repression) genes. In line with nuclear import of Gln3 being under control of TOR and dephosphorylation by the Sit4 phosphatase, we identify novel TOR-sensitive sit4 mutations that confer rapamycin resistance and importantly, mislocalise Gln3 when TOR is inhibited. This is similar to gln3Δ cells, which abolish the rapamycin hypersensitivity of U34 modification mutants, and suggests TOR deregulation due to tRNA undermodification operates through Gln3. In line with this, loss of U34 modifications (elp3Δ, urm1Δ) enhances nuclear import of and NCR gene activation (MEP2, GAP1) by Gln3 when TOR activity is low. Strikingly, this stimulatory effect onto Gln3 is suppressed by overexpression of tRNAs that usually carry the U34 modifications. Collectively, our data suggest that proper TOR signaling requires intact tRNA modifications and that loss of U34 modifications impinges on the TORsensitive NCR branch via Gln3 misregulation.

Loss of Anticodon Wobble Uridine Modifications Affects tRNALys Function and Protein Levels in Saccharomyces cerevisiae

In eukaryotes, wobble uridines in the anticodons of tRNALysUUU, tRNAGluUUC and tRNAGlnUUG are modified to 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U). While mutations in subunits of the Elongator complex (Elp1-Elp6), which disable mcm5 side chain formation, or removal of components of the thiolation pathway (Ncs2/Ncs6, Urm1, Uba4) are individually tolerated, the combination of both modification defects has been reported to have lethal effects on Saccharomyces cerevisiae. Contrary to such absolute requirement of mcm5s2U for viability, we demonstrate here that in the S. cerevisiae S288C-derived background, both pathways can be simultaneously inactivated, resulting in combined loss of tRNA anticodon modifications (mcm5U and s2U) without a lethal effect. However, an elp3 disruption strain displays synthetic sick interaction and synergistic temperature sensitivity when combined with either uba4 or urm1 mutations, suggesting major translational defects in the absence of mcm5s2U modifications. Consistent with this notion, we find cellular protein levels drastically decreased in an elp3uba4 double mutant and show that this effect as well as growth phenotypes can be partially rescued by excess of tRNALysUUU. These results may indicate a global translational or protein homeostasis defect in cells simultaneously lacking mcm5 and s2 wobble uridine modification that could account for growth impairment and mainly originates from tRNALysUUU hypomodification and malfunction.

Composition and stability of organic matter fractions in soils under different land use regimes

Soil organic matter (SOM) vitally impacts all soil functions and plays a key role in the global carbon (C) cycle. More than 70% of the terrestric C stocks that participate in the active C cycle are stored in the soil. Therefore, quantitative knowledge of the rates of C incorporation into SOM fractions of different residence time is crucial to understand and predict the sequestration and stabilization of soil organic carbon (SOC). Consequently, there is a need of fractionation procedures that are capable of isolating functionally SOM fractions, i.e. fractions that are defined by their stability. The literature generally refers to three main mechanisms of SOM stabilization: protection of SOM from decomposition by (i) its structural composition, i.e. recalcitrance, (ii) spatial inaccessibility and/or (iii) interaction with soil minerals and metal ions. One of the difficulties in developing fractionation procedures for the isolation of functional SOM fractions is the marked heterogeneity of the soil environment with its various stabilization mechanisms – often several mechanisms operating simultaneously – in soils and soil horizons of different texture and mineralogy. The overall objective of the present thesis was to evaluate present fractionation techniques and to get a better understanding of the factors of SOM sequestration and stabilization. The first part of this study is attended to the structural composition of SOM. Using 13C cross-polarization magic-angle spinning (CPMAS) nuclear magnetic resonance (NMR) spectroscopy, (i) the effect of land use on SOM composition was investigated and (ii) examined whether SOM composition contributes to the different stability of SOM in density and aggregate fractions. The second part of the present work deals with the mineral-associated SOM fraction. The aim was (iii) to evaluate the suitability of chemical fractionation procedures used in the literature for the isolation of stable SOM pools (stepwise hydrolysis, treatments using oxidizing agents like Na2S2O8, H2O2, and NaOCl as well as demineralization of the residue obtained by the NaOCl treatment using HF (NaOCl+HF)) by pool sizes, 13C and 14C data. Further, (iv) the isolated SOM fractions were compared to the inert organic matter (IOM) pool obtained for the investigated soils using the Rothamsted Carbon Model and isotope data in order to see whether the tested chemical fractionation methods produce SOM fractions capable to represent this pool. Besides chemical fractionation, (v) the suitability of thermal oxidation at different temperatures for obtaining stable SOC pools was evaluated. Finally, (vi) the short-term aggregate dynamics and the factors that impact macroaggregate formation and C stabilization were investigated by means of an incubation study using treatments with and without application of 15N labeled maize straw of different degradability (leaves and coarse roots). All treatments were conducted with and without the addition of fungicide. Two study sites with different soil properties and land managements were chosen for these investigations. The first one, located at Rotthalmünster, is a Stagnic Luvisol (silty loam) under different land use regimes. The Ah horizons of a spruce forest and continuous grassland and the Ap and E horizons of two plots with arable crops (continuous maize and wheat cropping) were examined. The soil of the second study site, located at Halle, is a Haplic Phaeozem (loamy sand) where the Ap horizons of two plots with arable crops (continuous maize and rye cropping) were investigated. Both study sites had a C3-/C4-vegetational change on the maize plot for the purpose of tracing the incorporation of the younger, maize-derived C into different SOM fractions and the calculation of apparent C turnover times of these. The Halle site is located near a train station and industrial areas, which caused a contamination with high amounts of fossil C. The investigation of aggregate and density fractions by 13C CPMAS NMR spectroscopy revealed that density fractionation isolated SOM fractions of different composition. The consumption of a considerable part (10–20%) of the easily available O-alkyl-C and the selective preservation of the more recalcitrant alkyl-C when passing from litter to the different particulate organic matter (POM) fractions suggest that density fractionation was able to isolate SOM fractions with different degrees of decomposition. The spectra of the aggregate fractions resembled those of the mineral-associated SOM fraction obtained by density fractionation and no considerable differences were observed between aggregate size classes. Comparison of plant litter, density and aggregate size fractions from soil under different land use showed that the type of land use markedly influenced the composition of SOM. While SOM of the acid forest soil was characterized by a large content (> 50%) of POM, which contained high amounts of spruce-litter derived alkyl-C, the organic matter in the biologically more active grassland and arable soils was dominated by mineral-associated SOM (> 95%). This SOM fraction comprised greater proportions of aryl- and carbonyl-C and is considered to contain a higher amount of microbially-derived organic substances. Land use can alter both, structure and stability of SOM fractions. All applied chemical treatments induced considerable SOC losses (> 70–95% of mineral-associated SOM) in the investigated soils. The proportion of residual C after chemical fractionation was largest in the arable Ap and E horizons and increased with decreasing C content in the initial SOC after stepwise hydrolysis as well as after the oxidative treatments with H2O2 and Na2S2O8. This can be expected for a functional stable pool of SOM, because it is assumed that the more easily available part of SOC is consumed first if C inputs decrease. All chemical treatments led to a preferential loss of the younger, maize-derived SOC, but this was most pronounced after the treatments with Na2S2O8 and H2O2. After all chemical fractionations, the mean 14C ages of SOC were higher than in the mineral-associated SOM fraction for both study sites and increased in the order: NaOCl < NaOCl+HF ≤ stepwise hydrolysis << H2O2 ≈ Na2S2O8. The results suggest that all treatments were capable of isolating a more stable SOM fraction, but the treatments with H2O2 and Na2S2O8 were the most efficient ones. However, none of the chemical fractionation methods was able to fit the IOM pool calculated using the Rothamsted Carbon Model and isotope data. In the evaluation of thermal oxidation for obtaining stable C fractions, SOC losses increased with temperature from 24–48% (200°C) to 100% (500°C). In the Halle maize Ap horizon, losses of the young, maize-derived C were considerably higher than losses of the older C3-derived C, leading to an increase in the apparent C turnover time from 220 years in mineral-associated SOC to 1158 years after thermal oxidation at 300°C. Most likely, the preferential loss of maize-derived C in the Halle soil was caused by the presence of the high amounts of fossil C mentioned above, which make up a relatively large thermally stable C3-C pool in this soil. This agrees with lower overall SOC losses for the Halle Ap horizon compared to the Rotthalmünster Ap horizon. In the Rotthalmünster soil only slightly more maize-derived than C3-derived SOC was removed by thermal oxidation. Apparent C turnover times increased slightly from 58 years in mineral-associated SOC to 77 years after thermal oxidation at 300°C in the Rotthalmünster Ap and from 151 to 247 years in the Rotthalmünster E horizon. This led to the conclusion that thermal oxidation of SOM was not capable of isolating SOM fractions of considerably higher stability. The incubation experiment showed that macroaggregates develop rapidly after the addition of easily available plant residues. Within the first four weeks of incubation, the maximum aggregation was reached in all treatments without addition of fungicide. The formation of water-stable macroaggregates was related to the size of the microbial biomass pool and its activity. Furthermore, fungi were found to be crucial for the development of soil macroaggregates as the formation of water-stable macroaggregates was significantly delayed in the fungicide treated soils. The C concentration in the obtained aggregate fractions decreased with decreasing aggregate size class, which is in line with the aggregate hierarchy postulated by several authors for soils with SOM as the major binding agent. Macroaggregation involved incorporation of large amounts maize-derived organic matter, but macroaggregates did not play the most important role in the stabilization of maize-derived SOM, because of their relatively low amount (less than 10% of the soil mass). Furthermore, the maize-derived organic matter was quickly incorporated into all aggregate size classes. The microaggregate fraction stored the largest quantities of maize-derived C and N – up to 70% of the residual maize-C and -N were stored in this fraction.

Impact of sward type, cutting date and conditioning temperature on mass and energy flows in the integrated generation of solid fuel and biogas from semi-natural grassland

Energy production from biomass and the conservation of ecologically valuable grassland habitats are two important issues of agriculture today. The combination of a bioenergy production, which minimises environmental impacts and competition with food production for land with a conversion of semi-natural grasslands through new utilization alternatives for the biomass, led to the development of the IFBB process. Its basic principle is the separation of biomass into a liquid fraction (press fluid, PF) for the production of electric and thermal energy after anaerobic digestion to biogas and a solid fraction (press cake, PC) for the production of thermal energy through combustion. This study was undertaken to explore mass and energy flows as well as quality aspects of energy carriers within the IFBB process and determine their dependency on biomass-related and technical parameters. Two experiments were conducted, in which biomass from semi-natural grassland was conserved as silage and subjected to a hydrothermal conditioning and a subsequent mechanical dehydration with a screw press. Methane yield of the PF and the untreated silage was determined in anaerobic digestion experiments in batch fermenters at 37°C with a fermentation time of 13-15 and 27-35 days for the PF and the silage, respectively. Concentrations of dry matter (DM), ash, crude protein (CP), crude fibre (CF), ether extract (EE), neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent ligning (ADL) and elements (K, Mg, Ca, Cl, N, S, P, C, H, N) were determined in the untreated biomass and the PC. Higher heating value (HHV) and ash softening temperature (AST) were calculated based on elemental concentration. Chemical composition of the PF and mass flows of all plant compounds into the PF were calculated. In the first experiment, biomass from five different semi-natural grassland swards (Arrhenaterion I and II, Caricion fuscae, Filipendulion ulmariae, Polygono-Trisetion) was harvested at one late sampling (19 July or 31 August) and ensiled. Each silage was subjected to three different temperature treatments (5°C, 60°C, 80°C) during hydrothermal conditioning. Based on observed methane yields and HHV as energy output parameters as well as literature-based and observed energy input parameters, energy and green house gas (GHG) balances were calculated for IFBB and two reference conversion processes, whole-crop digestion of untreated silage (WCD) and combustion of hay (CH). In the second experiment, biomass from one single semi-natural grassland sward (Arrhenaterion) was harvested at eight consecutive dates (27/04, 02/05, 09/05, 16/05, 24/05, 31/05, 11/06, 21/06) and ensiled. Each silage was subjected to six different treatments (no hydrothermal conditioning and hydrothermal conditioning at 10°C, 30°C, 50°C, 70°C, 90°C). Energy balance was calculated for IFBB and WCD. Multiple regression models were developed to predict mass flows, concentrations of elements in the PC, concentration of organic compounds in the PF and energy conversion efficiency of the IFBB process from temperature of hydrothermal conditioning as well as NDF and DM concentration in the silage. Results showed a relative reduction of ash and all elements detrimental for combustion in the PC compared to the untreated biomass of 20-90%. Reduction was highest for K and Cl and lowest for N. HHV of PC and untreated biomass were in a comparable range (17.8-19.5 MJ kg-1 DM), but AST of PC was higher (1156-1254°C). Methane yields of PF were higher compared to those of WCD when the biomass was harvested late (end of May and later) and in a comparable range when the biomass was harvested early and ranged from 332 to 458 LN kg-1 VS. Regarding energy and GHG balances, IFBB, with a net energy yield of 11.9-14.1 MWh ha-1, a conversion efficiency of 0.43-0.51, and GHG mitigation of 3.6-4.4 t CO2eq ha-1, performed better than WCD, but worse than CH. WCD produces thermal and electric energy with low efficiency, CH produces only thermal energy with a low quality solid fuel with high efficiency, IFBB produces thermal and electric energy with a solid fuel of high quality with medium efficiency. Regression models were able to predict target parameters with high accuracy (R2=0.70-0.99). The influence of increasing temperature of hydrothermal conditioning was an increase of mass flows, a decrease of element concentrations in the PC and a differing effect on energy conversion efficiency. The influence of increasing NDF concentration of the silage was a differing effect on mass flows, a decrease of element concentrations in the PC and an increase of energy conversion efficiency. The influence of increasing DM concentration of the silage was a decrease of mass flows, an increase of element concentrations in the PC and an increase of energy conversion efficiency. Based on the models an optimised IFBB process would be obtained with a medium temperature of hydrothermal conditioning (50°C), high NDF concentrations in the silage and medium DM concentrations of the silage.