A molecular level understanding of the thermodynamics and kinetics of the chemical bonding between mercury, Hg(II), and natural organic matter (NOM) associated thiol functional groups (NOM-RSH) is required if bioavailability and transformation processes of Hg in the environment are to be fully understood. This study provides the thermodynamic stability of the Hg(NOM-RS) structure using a robust method in which cysteine (Cys) served as a competing ligand to NOM (Suwannee River 2R101N sample) associated RSH groups. The concentration of the latter was quantified to be 7.5 ± 0.4 μmol g NOM by Hg L-edge EXAFS spectroscopy. The Hg(Cys) molecule concentration in chemical equilibrium with the Hg(II)-NOM complexes was directly determined by HPLC-ICPMS and losses of free Cys due to secondary reactions with NOM was accounted for in experiments using H NMR spectroscopy andC isotope labeled Cys. The log K ± SD for the formation of the Hg(NOM-RS) molecular structure, Hg + 2NOM-RS = Hg(NOM-RS), and for the Hg(Cys)(NOM-RS) mixed complex, Hg + Cys + NOM-RS = Hg(Cys)(NOM-RS), were determined to be 40.0 ± 0.2 and 38.5 ± 0.2, respectively, at pH 3.0. The magnitude of these constants was further confirmed by H NMR spectroscopy and the Hg(NOM-RS) structure was verified by Hg L-edge EXAFS spectroscopy. An important finding is that the thermodynamic stabilities of the complexes Hg(NOM-RS), Hg(Cys)(NOM-RS) and Hg(Cys) are very similar in magnitude at pH values <7, when all thiol groups are protonated. Together with data on 15 low molecular mass (LMM) thiols, as determined by the same method ( Liem-Ngyuen et al. Thermodynamic stability of mercury(II) complexes formed with environmentally relevant low-molecular-mass thiols studied by competing ligand exchange and density functional theory . Environ. Chem. 2017 , 14 , ( 4 ), 243 - 253 .), the constants for Hg(NOM-RS) and Hg(Cys)(NOM-RS) represent an internally consistent thermodynamic data set that we recommend is used in studies where the chemical speciation of Hg(II) is determined in the presence of NOM and LMM thiols.

Conformational change is regulating the biological activity of a large number of proteins and enzymes. Efforts in structural biology have provided molecular descriptions of the interactions that stabilize the stable ground states on the reaction trajectories during conformational change. Less is known about equilibrium thermodynamic stabilities of the polypeptide segments that participate in structural changes and whether the stabilities are relevant for the reaction pathway. Adenylate kinase (Adk) is composed of three subdomains: CORE, ATPlid, and AMPbd. ATPlid and AMPbd are flexible nucleotide binding subdomains where large-scale conformational changes are directly coupled to catalytic activity. In this report, the equilibrium thermodynamic stabilities of Adk from both mesophilic and hyperthermophilic bacteria were investigated using solution state NMR spectroscopy together with protein engineering experiments. Equilibrium hydrogen to deuterium exchange experiments indicate that the flexible subdomains are of significantly lower thermodynamic stability compared to the CORE subdomain. Using site-directed mutagenesis, parts of ATPlid and AMPbd could be selectively unfolded as a result of perturbation of hydrophobic clusters located in these respective subdomains. Analysis of the perturbed Adk variants using NMR spin relaxation and C(alpha) chemical shifts shows that the CORE subdomain can fold independently of ATPlid and AMPbd; consequently, folding of the two flexible subdomains occurs independently of each other. Based on the experimental results it is apparent that the flexible subdomains fold into their native structure in a noncooperative manner with respect to the CORE subdomain. These results are discussed in light of the catalytically relevant conformational change of ATPlid and AMPbd.

Soil processes in high-latitude regions during winter are important contributors to global carbon circulation, but our understanding of the mechanisms controlling these processes is poor and observed temperature response coefficients of CO 2 production in frozen soils deviate markedly from thermodynamically predicted responses (sometimes by several orders of magnitude). We investigated the temperature response of CO 2 production in 23 unfrozen and frozen surface soil samples from various types of boreal forests and peatland ecosystems and also measured changes in water content in them after freezing. We demonstrate that deviations in temperature responses at subzero temperatures primarily emanates from water deficiency caused by freezing of the soil water, and that the amount of unfrozen water is mainly determined by the quality of the soil organic matter, which is linked to the vegetation cover. Factoring out the contribution of water limitation to the CO 2 temperature responses yields response coefficients that agree well with expectations based on thermodynamic theory concerning biochemical temperature responses. This partitioning between a pure temperature response and the effect of water availability on the response of soil CO 2 production at low temperatures is crucial for a thorough understanding of low-temperature soil processes and for accurate predictions of C-balances in northern terrestrial ecosystems.

A large proportion of the global soil carbon pool is stored in soils of high-latitude ecosystems in which microbial processes and production of greenhouse gases proceed during the winter months. It has been suggested that microorganisms have limited ability to sequester substrates at temperatures around and below 0°C and that a metabolic shift to dominance of catabolic processes occurs around these temperatures. However, there are contrary indications that anabolic processes can proceed, because microbial growth has been observed at far lower temperatures. Therefore, we investigated the utilization of the microbial substrate under unfrozen and frozen conditions in a boreal forest soil across a temperature range from −9°C to +9°C, by using gas chromatography-isotopic ratio mass spectrometry and 13 C magic-angle spinning NMR spectroscopy to determine microbial turnover and incorporation of 13 C-labeled glucose. Our results conclusively demonstrate that the soil microorganisms maintain both catabolic (CO 2 production) and anabolic (biomass synthesis) processes under frozen conditions and that no significant differences in carbon allocation from [ C-compounds occurred between +9°C and −4°C. The only significant metabolic changes detected were increased fluidity of the cell membranes synthesized at frozen conditions and increased production of glycerol in the frozen samples. The finding that the processes in frozen soil are similar to those in unfrozen soil has important implications for our general understanding and conceptualization of soil carbon dynamics in high-latitude ecosystems.soil organic matter mineralization |

BackgroundLignocellulose from fast growing hardwood species is a preferred source of polysaccharides for advanced biofuels and “green” chemicals. However, the extensive acetylation of hardwood xylan hinders lignocellulose saccharification by obstructing enzymatic xylan hydrolysis and causing inhibitory acetic acid concentrations during microbial sugar fermentation. To optimize lignocellulose for cost-effective saccharification and biofuel production, an acetyl xylan esterase AnAXE1 from Aspergillus niger was introduced into aspen and targeted to cell walls.Results AnAXE1-expressing plants exhibited reduced xylan acetylation and grew normally. Without pretreatment, their lignocellulose yielded over 25% more glucose per unit mass of wood (dry weight) than wild-type plants. Glucose yields were less improved (+7%) after acid pretreatment, which hydrolyses xylan. The results indicate that AnAXE1 expression also reduced the molecular weight of xylan, and xylan–lignin complexes and/or lignin co-extracted with xylan, increased cellulose crystallinity, altered the lignin composition, reducing its syringyl to guaiacyl ratio, and increased lignin solubility in dioxane and hot water. Lignin-associated carbohydrates became enriched in xylose residues, indicating a higher content of xylo-oligosaccharides.ConclusionsThis work revealed several changes in plant cell walls caused by deacetylation of xylan. We propose that deacetylated xylan is partially hydrolyzed in the cell walls, liberating xylo-oligosaccharides and their associated lignin oligomers from the cell wall network. Deacetylating xylan thus not only increases its susceptibility to hydrolytic enzymes during saccharification but also changes the cell wall architecture, increasing the extractability of lignin and xylan and facilitating saccharification.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0782-4) contains supplementary material, which is available to authorized users.