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Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone
Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi ‘omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments through a shift towards carbohydrate-utilizing metabolic pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C content only (explaining 67% vs. 42% of variation), and bulk C did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.
Foliar isotopic and elemental biochemistry and leaf mass per area (LMA), Parque Natural Metropolitano, Panama, 2022
Foliar N and C isotope composition, bulk elemental N and C composition, and leaf mass per area (LMA) for leaves sampled from the Parque Natural Metropolitano (PNM), Panama, from January to April 2022 are presented. Measurements were made on leaves from 17 different tree, shrub and liana species, from sunlit canopy and understory locations on 8 vertical profiles. Full sample details and leaf area index (LAI) from the vertical profiles at PNM are also included in the data package. The aim of this measurement campaign was two-fold: to improve our understanding of the vertical variation in leaf-level water use efficiency, and to improve models which can predict leaf traits from leaf contact spectral measurements. Biochemistry data and sample metadata are presented in .csv files. The original isotopic data report, which includes details about standards and data accuracy, is provided in .xlsx format. Data and metadata meet the ESS-DIVE reporting format requirements for file level metadata (FLMD) and comma separated values (csv). The protocol details are provided as pdf documents. In addition to foliar biochemistry data reported here these samples were also used for measurement of leaf gas exchange, and leaf optical properties. These data can be linked using the unique sample ID and are provided in separate data packages (NGT0192 and NGT0193).
Bacterial Volatile Organic Compounds as a Strategy to Increase Drought Tolerance in Maize (Zea mays L.): Influence on Plant Biochemistry
Maize is highly susceptible to drought, which affects growth and yield. This study investigated how bacterial volatile organic compounds (BVOCs) affect maize drought tolerance. Drought reduced shoot size but increased root length, an adaptation for accessing deeper soil moisture. BVOCs from strain D12 significantly increased root length and shoot growth under drought conditions. Drought also altered root biochemistry, decreasing enzyme activity, and increased osmolyte levels. BVOCs from strains F11 and FS4-14 further increased osmolyte levels but did not protect membranes from oxidative damage, while BVOCs from strains D12 and D7 strains reduced osmolyte levels and cell damage. In shoots, drought increased the levels of osmolytes and oxidative stress markers. BVOCs from FS4-14 had minimal effects on shoot biochemistry. BVOCs from D12 and F11 partially restored metabolic activity but did not reduce cell damage. BVOCs from D7 reduced metabolic activity and cell damage. These results suggest that BVOCs can modulate the biochemical response of maize to drought, with some strains evidencing the potential to enhance drought tolerance.
Tight Coupling of Surface and In-Plant Biochemistry and Convection Governs Key Fine Particulate Components over the Amazon Rainforest
We report that throughout the troposphere over the Amazon rainforest, isoprene epoxydiol-secondary organic aerosols (IEPOX-SOA) are key components of submicrometer particle mass. IEPOX-SOA is thought to form by multiphase chemical pathways in the atmosphere, but using detailed model simulations, we show that these pathways are strongly inhibited by the solid particle phase state prevailing in the upper troposphere. We find that 2-methyltetrol gases formed by in-plant biochemical oxidation pathways, their partitioning to fine particles, and dissolution in cloud droplets can explain over 90% of IEPOX-SOA mass concentrations in the upper troposphere. In agreement with previous PM10 chiral measurements, our simulations indicate that plant biochemical processes are the dominant source of particulate 2-methyltetrols in the lower troposphere as well (>70%). Our results imply that in-plant biochemistry plays a central but previously unidentified role in aerosol processes and atmosphere-biosphere-climate interactions over the rainforest.
An update on oxysterol biochemistry: New discoveries in lipidomics
Highlights: • Oxysterols can regulate both the innate and adaptive immune systems. • Oxysterols can be tumour suppressors and on cometabolites. • Oxysterols can inhibit or activate the Hh signalling pathway. Oxysterols are oxidised derivatives of cholesterol or its precursors post lanosterol. They are intermediates in the biosynthesis of bile acids, steroid hormones and 1,25-dihydroxyvitamin D{sub 3.} Although often considered as metabolic intermediates there is a growing body of evidence that many oxysterols are bioactive and their absence or excess may be part of the cause of a disease phenotype. Using global lipidomics approaches oxysterols are underrepresented encouraging the development of targeted approaches. In this article, we discuss recent discoveries important in oxysterol biochemistry and some of the targeted lipidomic approaches used to make these discoveries.
Cell-free synthetic biochemistry upgrading of ethanol to 1,3 butanediol
It is now possible to efficiently fix flue gas CO/CO 2 into ethanol using acetogens, thereby making carbon negative ethanol. While the ethanol could be burned as a fuel, returning the CO 2 to the atmosphere, it might also be possible to use the fixed carbon in more diverse chemicals, thereby keeping it fixed. Here we describe a simple synthetic biochemistry approach for converting carbon negative ethanol into the synthetic building block chemical 1,3 butanediol (1,3-BDO). The pathway completely conserves carbon from ethanol and can ultimately be powered electrochemically via formate oxidation. Our proof-of-principle system reached a maximum productivity of 0.16 g/L/h and, with replenishment of feedstock and enzymes, achieved a titer of 7.7 g/L. We identify a number of elements that can be addressed in future work to improve both cell-free and cell-based production of 1,3-BDO.
Peripheral blood hematology, plasma biochemistry, and the optimization of an in vitro immune-based assay in the brown watersnake ( Nerodia taxispilota )
Reptiles represent a phylogenetic lineage that provides a unique link between ectothermic anamniotes and endothermic amniotes. Compared to mammalian and avian species, our understanding of the reptilian immune system is greatly lacking. This gap in knowledge is largely due to an absence of established immune-based assays or specific reagents for these species. In the present study, brown watersnakes (Nerodia taxispilota) were live-captured in the wild, sexed, weighed, measured, bled via the caudal vein and released. At 24 hr post-collection, peripheral blood leukocytes were enriched and evaluated with an established mammalian in-vitro lymphocyte proliferation assay. Snake peripheral blood leukocyte enrichment yielded > 90% lymphocytes with viabilities averaging 81.5%. Baseline physiologic data for N. taxispilota, including hematology and total solids, leukocyte differentials, cell recovery and plasma biochemistry, were also collected. Cells cultured with Concanavalin A exhibited significantly increased proliferation at both 72 and 96 hr. Furthermore, these preliminary results show that enriched peripheral blood from wild-caught N. taxispilota provides a sufficient yield of leukocytes that can be cultured and functionally evaluated using a standard mammalian in-vitro immune-based assay.
Mesophyll conductance response to short-term changes in p CO 2 is related to leaf anatomy and biochemistry in diverse C 4 grasses
Mesophyll CO 2 conductance (g m ) in C 3 species responds to short-term (minutes) changes in environment potentially due to changes in leaf anatomical and biochemical properties and measurement artefacts. Compared with C 3 species, there is less information on g m responses to short-term changes in environmental conditions such as partial pressure of CO 2 (pCO 2 ) across diverse C 4 species and the potential determinants of these responses. Using 16 C 4 grasses we investigated the response of g m to short-term changes in pCO 2 and its relationship with leaf anatomy and biochemistry. In general, g m increased as pCO 2 decreased (statistically significant increase in 12 species), with percentage increases in gm ranging from +13% to +250%. Greater increase in g m at low pCO 2 was observed in species exhibiting relatively thinner mesophyll cell walls along with greater mesophyll surface area exposed to intercellular air spaces, leaf N, photosynthetic capacity and activities of phosphoenolpyruvate carboxylase and Rubisco. Species with greater CO 2 responses of g m were also able to maintain their leaf water-use efficiencies (TE i ) under low CO 2 . Our study advances understanding of CO 2 response of g m in diverse C 4 species, identifies the key leaf traits related to this response and has implications for improving C 4 photosynthetic models and TE i through modification of g m .
Stomatal conductance, not biochemistry, drives low temperature acclimation of photosynthesis in Populus balsamifera , regardless of nitrogen availability
Low temperature thermal acclimation may require adjustments to nitrogen and water use to sustain photosynthesis due to slow enzyme functioning and high-water viscosity. However, understanding of photosynthetic acclimation to temperatures below 11°C is limited. Here, we acclimated Populus balsamifera to 6 °C and 10 °C (6A and 10A, respectively) and provided the trees with either high or low N fertilizer. We measured net CO 2 assimilation rates (A net ), stomatal conductance (g s ), maximum rates of Rubisco carboxylation (V cmax ) and electron transport (J max ), and dark respiration (R d ) at leaf temperatures of 2, 6, 10, 14 and 18 °C, along with leaf N concentrations. The 10A trees had higher A net than the 6A trees at warmer leaf temperatures, which was correlated with higher g s in the 10A trees. The instantaneous temperature responses of V cmax , J max and R d were similar for trees from both acclimation temperatures. While soil N availability increased leaf N concentrations, this had no effect on acclimation of photosynthesis or respiration. Our results indicate that acclimation below 11°C occurred primarily through changes in stomatal conductance, not photosynthetic biochemistry, and was unaffected by short-term N supply. Thermal acclimation of stomatal conductance should therefore be a priority for future carbon cycle model development.
Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of Tyrannosaurus rex
Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, this research is commonly met with skepticism, as the long standing dogma persists that such preservation in very deep time (>1 Ma) is unlikely. The Late Cretaceous dinosaur Tyrannosaurus rex (MOR 1125) has been shown, through multiple biochemical studies, to preserve original bone chemistry. Here, we provide additional, independent support that deep time bimolecular preservation is possible. We use synchrotron X-ray fluorescence imaging (XRF) and X-ray absorption spectroscopy (XAS) to investigate a section from the femur of this dinosaur, and demonstrate preservation of elements (S, Ca, and Zn) associated with bone remodeling and redeposition. We then compare these data to the bone of an extant dinosaur (bird), as well as a second non-avian dinosaur, Tenontosaurus tilletti (OMNH 34784) that did not preserve any sign of original biochemistry. Our data indicate that MOR 1125 bone cortices have similar bone elemental distributions to that of an extant bird, which supports preservation of original endogenous chemistry in this specimen.
Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes
Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts are very similar, Flag-CSN pulldowns are a proper alternative to CSN preparation from erythrocytes.
Metabolite discovery: Biochemistry’s scientific driver
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Microalgal lipids: biochemistry and biotechnology
Microalgae, including cyanobacteria, are a genetically diverse and biochemically diverse group of mostly photosynthetic organisms that can be found in nearly every ecosystem. They produce a broad range of compounds, including structural and bioactive lipids with various roles in the metabolism of the cell and potential applications in biotechnology. Here, the majority of lipids are synthesized in the chloroplast using acetate to produce fatty acids and terpenoids via the acetate pathway and methylerythritol phosphate deoxy-xylulose phosphate pathway, respectively. This review will highlight the major groups of microalgal lipids as well as their applications in food, fuels, and specialty chemicals. Future directions include the development of microalgal chassis organisms and molecular tools to manipulate lipid synthesis for the enhanced production of target metabolites.
Plant biochemistry influences tropospheric ozone formation, destruction, deposition, and response
Tropospheric ozone (O 3 ) is among the most damaging air pollutant to plants. Plants alter the atmospheric O 3 concentration in two distinct ways: (i) by the emission of volatile organic compounds (VOCs) that are precursors of O 3 ; and (ii) by dry deposition, which includes diffusion of O 3 into vegetation through stomata and destruction by nonstomatal pathways. Isoprene, monoterpenes, and higher terpenoids are emitted by plants in quantities that alter tropospheric O 3 . Deposition of O 3 into vegetation is related to stomatal conductance, leaf structural traits, and the detoxification capacity of the apoplast. The biochemical fate of O 3 once it enters leaves and reacts with aqueous surfaces is largely unknown, but new techniques for the tracking and identification of initial products have the potential to open the black box.
A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system
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Redox Biochemistry of Energy Conservation in Methanogens and their Syntrophic Partners
The primary objective of this project was to uncover previously unknown modes by which living organisms harvested energy. Specifically, it queried microbial systems, which were once thought to not be able to utilize oxygen. Through the use of cutting-edge approaches, we were able to identify novel mechanistic processes that allow organisms to thrive under varying environmental conditions. This constitutes a paradigm shift in the field. Our work has opened new vistas for expanding the horizons of energy conservation in biological systems, as well as shed light on green energy innovations.