Validation of a metabolite-GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases.

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa, a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. We focus on uridine diphosphate-glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa, presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.

Historic and Modern Approaches for the Discovery of Abandoned Wells for Methane Emissions Mitigation in Oil Creek State Park, Pennsylvania.

Hundreds of oil wells were drilled along Oil Creek in Pennsylvania in the mid-1800s, birthing the modern oil industry. No longer in operation, many wells are now classified as abandoned, and, due to their age, their locations are either unknown or inaccurately recorded. These historic-well sites present environmental, safety, and economic concerns in the form of possible methane leaks and physical hazards. Airborne magnetic and LiDAR surveys were conducted in the Pioneer Run watershed in Oil Creek State Park to find abandoned wells in a historically significant but physically challenging location. Wells were drilled in this area prior to modern geolocation and legal documentation. Although a large number of old wells were abandoned summarily without remediation of the site, much of the land area within Oil Creek State Park is now covered in trees and dense underbrush, which can obscure wellheads. The thick vegetation and steep terrain limited the possibility of ground-based surveys to easily find well sites for methane emissions studies. The data from remote sensing surveys were used to corroborate potential well locations from historic maps and photographs. Potential well sites were verified in a ground-based field survey and monitored for methane emissions. Two historic photographs documenting oil activity in the late 1800s were georeferenced using a combination of magnetic and LiDAR data. LiDAR data, which were more useful in georeferencing and in field verification, identified 290 field locations in the Pioneer Run watershed, 86% of which were possible well sites. Sixty-two percent of the ground-verified wells remained unplugged and comprised the majority of leaking wells. The mean methane emissions factor for unplugged wells was 0.027 ± 0.099 kg/day, lower than other Appalachian Basin methane emissions estimates. LiDAR was used for the first time, in combination with an airborne magnetic survey, to reveal underground oil industry features and inform well identification and remediation efforts in difficult-to-navigate regions. In the oldest oil fields, where well casing has been removed or wood conductor casing was installed, historic photographs provide additional lines of evidence for oil wells where ground disturbances have concealed surface features. Identification of well sites is necessary for mitigation efforts, as unplugged wells emit methane, a potent greenhouse gas.

Historic and modern approaches for discovery of abandoned wells for methane emissions mitigation in Oil Creek State Park, Pennsylvania.

BACKGROUND: Hundreds of oil wells were drilled along Oil Creek in Pennsylvania in the mid-1800s, birthing the modern oil industry. No longer in operation, many wells are now classified as abandoned, and, due to their age, their locations are either unknown or inaccurately recorded. These historic well sites present environmental, safety, and economic concerns in the form of possible methane leaks and physical hazards. METHODS: Airborne magnetic and LiDAR surveys were conducted in the Pioneer Run watershed in Oil Creek State Park to find abandoned wells in a historically significant but physically challenging location. Wells were drilled in this area prior to modern geolocation and legal documentation. Although a large number of old wells were abandoned summarily without remediation of the site, much of the land area within Oil Creek State Park is now covered in trees and dense underbrush, which can obscure wellheads. The thick vegetation and steep terrain limited the possibility of ground-based surveys to easily find well sites for methane emissions studies. The data from remote sensing surveys were used to corroborate potential well locations from historic maps and photographs. Potential well sites were verified in a ground-based field survey and monitored for methane emissions. RESULTS: Two historic photographs documenting oil activity in the late 1800s were georeferenced using a combination of magnetic and LiDAR data. LiDAR data, which were more useful in georeferencing and in field verification, identified 290 field locations in the Pioneer Run watershed, 86% of which were possible well sites. Sixty-two percent of the ground-verified wells remained unplugged and comprised the majority of leaking wells. The mean methane emissions factor for unplugged wells was 0.027 ± 0.099 kg/day, lower than other Appalachian Basin methane emissions estimates. CONCLUSIONS: LiDAR was used for the first time, in combination with an airborne magnetic survey, to reveal underground oil industry features and inform well identification and remediation efforts in difficult-to-navigate regions. In the oldest oil fields, where well casing has been removed or wood conductor casing was installed, historic photographs provide additional lines of evidence for oil wells where ground disturbances have concealed surface features. Identification of well sites is necessary for mitigation efforts, as unplugged wells emit methane, a potent greenhouse gas.

Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.

Identifying Abandoned Well Sites Using Database Records and Aeromagnetic Surveys.

Oil and natural gas are primary sources of energy in the United States. Improved drilling and extracting techniques have led to a renewed interest in historic oil and gas fields, but limited records of legacy wells make new drilling efforts more difficult, as abandoned wells may provide conduits for liquids and gases to migrate into groundwater reservoirs or the atmosphere. Well finding using aeromagnetic surveys pinpoints the location of steel-cased wells, detecting both active and abandoned wells, including buried casings lacking aboveground markers. Here, we present six aeromagnetic surveys conducted in Pennsylvania and Wyoming as case studies, comparing the magnetic points to locations known in databases. In all study sites, more magnetic points were detected than recorded in databases. Based on differences between theoretical database well counts and the actual number of wells detected in surveys, we estimated the total number of wells in Pennsylvania to be 395 000-466 000 and 181 000-182 000 in Wyoming. Extrapolating to the national level, we estimate the average number of wells in the continental United States is 6.04 ± 19.97 million wells with 1.16 ± 3.84 million of those designated as abandoned wells, within the range of previous abandoned well count estimations. Although aeromagnetic surveys are limited to detecting steel-cased wells and do not differentiate sites based on well status, this study nevertheless demonstrates the utility of aeromagnetic surveys in well finding efforts across the country and shows limitations in database records of oil and natural gas wells.

Beyond-the-Meter: Unaccounted Sources of Methane Emissions in the Natural Gas Distribution Sector.

The United States Environmental Protection Agency maintains an inventory of greenhouse gas emissions in accordance with the Intergovernmental Panel on Climate Change. Methane (CH4), a potent gas with a global warming potential 86-125× that of carbon dioxide (CO2) over a twenty-year period, is the main component of natural gas (NG). As NG becomes an increasingly larger percentage of the energy resources used in the United States, it is ever more important to evaluate the CH4 emissions inventory. However, the inventory also does not account for all possible sources of CH4 leaks, contributing to uncertainty in the national CH4 inventory. Discrepancies between top-down and bottom-up inventories of CH4 emissions imply that there are significant unaccounted-for sources of CH4 leaks, especially over cities. Diffuse CH4 plumes above cities that are not attributable to distribution pipelines or other NG infrastructure suggest many small beyond-the-meter leaks together contribute to large emissions. Here, we evaluate the distribution sector of the CH4 emissions inventory and make suggestions to improve the inventory by analyzing end-user emissions. Preliminary research into beyond-the-meter emissions suggests that while individually small, the appliances and buildings that make up the residential sector could contribute significantly to national scale emissions. Furnaces are the most leak-prone of appliances, contributing to 0.14% of total CH4 emissions from the NG sector in the United States. Combining measurements from whole house emissions and steady-state operation of appliances, we estimate that residential homes and appliances could release 9.1 Gg CH4 yearly in the United States, totaling over 2% of the CH4 released from the NG sector. While factors such as appliance age and usage, climate, and residential setting could influence the emissions profile of individual appliances, these preliminary estimates justify further exploration of beyond-the-meter emissions.

In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products.

Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product that exhibits extraordinarily narrow-spectrum antibacterial activity toward the causative agent of anthrax, Bacillus anthracis. During PZN biosynthesis, a cyclodehydratase catalyzes cyclization of cysteine, serine, and threonine residues in the PZN precursor peptide (BamA) to azolines. Subsequently, a dehydrogenase oxidizes most of these azolines to thiazoles and (methyl)oxazoles. The final biosynthetic steps consist of leader peptide removal and dimethylation of the nascent N-terminus. Using a heterologously expressed and purified heterocycle synthetase, the BamA peptide was processed in vitro concordant with the pattern of post-translational modification found in the naturally occurring compound. Using a suite of BamA-derived peptides, including amino acid substitutions as well as contracted and expanded substrate variants, the substrate tolerance of the heterocycle synthetase was elucidated in vitro, and the residues crucial for leader peptide binding were identified. Despite increased promiscuity compared to what was previously observed during heterologous production in E. coli, the synthetase retained exquisite selectivity in cyclization of unnatural peptides only at positions which correspond to those cyclized in the natural product. A cleavage site was subsequently introduced to facilitate leader peptide removal, yielding mature PZN variants after enzymatic or chemical dimethylation. In addition, we report the isolation and characterization of two novel PZN-like natural products that were predicted from genome sequences but whose production had not yet been observed.

Plantazolicin is an ultra-narrow spectrum antibiotic that targets the Bacillus anthracis membrane.

Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified natural product from Bacillus methylotrophicus FZB42 and Bacillus pumilus. Extensive tailoring to twelve of the fourteen amino acid residues in the mature natural product endows PZN with not only a rigid, polyheterocyclic structure, but also antibacterial activity. Here we report a remarkably discriminatory activity of PZN toward Bacillus anthracis, which rivals a previously-described gamma (γ) phage lysis assay in distinguishing B. anthracis from other members of the Bacillus cereus group. We evaluate the underlying cause of this selective activity by measuring the RNA expression profile of PZN-treated B. anthracis, which revealed significant upregulation of genes within the cell envelope stress response. PZN depolarizes the B. anthracis membrane like other cell envelope-acting compounds but uniquely localizes to distinct foci within the envelope. Selection and whole-genome sequencing of PZN-resistant mutants of B. anthracis implicate a relationship between the action of PZN and cardiolipin (CL) within the membrane. Exogenous CL increases the potency of PZN in wild type B. anthracis and promotes the incorporation of fluorescently tagged PZN in the cell envelope. We propose that PZN localizes to and exacerbates structurally compromised regions of the bacterial membrane, which ultimately results in cell lysis.

Insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin.

Peptide antibiotics represent a class of conformationally constrained natural products of growing pharmaceutical interest. Plantazolicin (PZN) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, Bacillus anthracis. The bioactivity of PZN is contingent on dimethylation of its N-terminal Arg residue by an S-adenosylmethionine-dependent methyltransferase. Here, we explore the substrate tolerances of two homologous PZN methyltransferases by carrying out kinetic analyses of the enzymes against a synthetic panel of truncated PZN analogs containing the N-terminal Arg residue. X-ray cocrystal structures of the PZN methyltransferases with each of these heterocycle-containing substrates provide a rationale for understanding the strict substrate specificity of these enzymes. Kinetic studies of structure-guided, site-specific variants allowed for the assignment of residues governing catalysis and substrate scope. Microbiological testing further revealed that upon dimethylation of the N-terminal Arg, a pentaheterocyclized PZN analog retained potent anti-B. anthracis activity, nearly equal to that of full-length PZN. These studies may be useful in the biosynthetic engineering of natural product analogs with different bioactivity profiles, as demonstrated by our identification of a truncated plantazolicin derivative that is active against methicillin-resistant Staphylococcus aureus (MRSA).

Synthesis of plantazolicin analogues enables dissection of ligand binding interactions of a highly selective methyltransferase.

A convergent strategy for the synthesis of truncated analogues of plantazolicin (PZN), a member of the thiazole/oxazole-modified microcin (TOMM) class of natural products, has been developed. These N-terminal mono-, tri-, and pentazole substructures of PZN were utilized to probe the substrate requirements and thermodynamic ligand binding parameters of an unusually selective PZN methyltransferase (BamL) by isothermal titration calorimetry. Our results demonstrate that the presence of a single N-terminal azole permits efficient processing by BamL; however, the substrate binding becomes stronger with increased polyazole chain length.